user13375: For purposes of this question I define “uncertainty” as a willingness to entertain doubt or acknowledge incomplete knowledge with regards to the truth of the matter about what one knows of a particular question of subject. And I define “the truth of the matter” as an objective fact about some aspect of reality which is independent of observer or context and is not contingent in any way.
For a long while I have regarded myself as unusually capable or comfortable with uncertainty. Having a general willingness to see the gray in every question and to acknowledge my own incomplete knowledge. To see and entertain the viewpoints of others and to grant that my own viewpoint is not certain. A general comfortability with complexity that is above average. And this is something I prided myself in thinking of as beneficial.
However, I recently realized that a lot of what I define as “uncertainty” presupposes an objective fact of the matter that is not contingent. And that it handcuffs me at times in that I can be of two, three, or more minds about something and unsure of the proper course to take.
Moreover, it occurred to me that this is not compatible with the doctrine of emptiness which I understand quite clearly as saying that for every conception that I have... it is not undergirded by a genuine non-contingent fact of the matter.
So with that...
Is uncertainty as defined above incompatible with emptiness?
If so, how? If so, what repercussions can be seen as occurring with this misunderstanding? What is an appropriate definition of uncertainty or one that is compatible with emptiness or how things really exist?
If not, why not? Where is the error in my thinking?
A question that might be related, but different is Is lack of doubt a form of self-cherishing?

user17655: 
Case 5 of the Mumonkan
  Kyõgen's "Man up in a Tree"              
Kyõgen Oshõ said, "It is like a man up in a tree hanging from a branch
  with his mouth; his hands grasp no bough, his feet rest on no limb.
Someone appears under the tree and asks him, 'What is the meaning of
  Bodhidharma's coming from the West?' If he does not answer, he fails
  to respond to the question. If he does answer, he will lose his life.
What would you do in such a situation?"
Mumon's Comment
Even if your eloquence flows like a river, it is of no avail.
Though you can expound the whole of Buddhist literature, it is of no
  use.
If you solve this problem, you will give life to the way that has been
  dead until this moment and destroy the way that has been alive up to
  now.
Otherwise you must wait for Maitreya Buddha and ask him.
Mumon's Verse
Kyõgen is truly thoughtless;
  His vice and poison are endless.
  He stops up the mouths of the monks,
  And devil's eyes sprout from their bodies.

So this part of your question struck me:

For a long while I have regarded myself as unusually capable or
  comfortable with uncertainty. Having a general willingness to see the
  gray in every question and to acknowledge my own incomplete knowledge.
  To see and entertain the viewpoints of others and to grant that my own
  viewpoint is not certain. A general comfortability with complexity
  that is above average. And this is something I prided myself in
  thinking of as beneficial.

I can't help but wonder if you've ever been truly uncertain.  Every shade of gray you see, every conflicting idea, is just another manifestation of certainty.  You can hold it in your mind, consider its merits, and weigh its value against what you already know.  Nothing here is really uncertain as all that you take to be uncertainty depends on preexisting conditions.  Every novel idea is just showing you what you already know albeit from a different point of view.  
What answer can you hope to hear when all of the Buddhas of past, present, and future have hung their mouths on the wall?  What words will save your life when you are hanging from a branch by your teeth?
Real doubt leaves us dumbfounded.  There is nothing comfortable about it.  The kind of doubt that stops up your head with cotton and hits you in the forehead like an unseen cabinet in a dark room is the kind of doubt that is truly productive.  There are no edges to hold onto.  Your previous ways of engaging the world won't help you move real doubt a single inch.  In that doubt, we are helpless and begging for our life.  We are desperate and unsure of which way to turn.  In the midst of such great doubt, we are also completely empty.
To see doubt is to see emptiness.  To see emptiness, we have to begin with doubt.  With faith and determination, both can resolve into wisdom. Only on the other side of great doubt can we hope to learn anything new.     

user43: 
When fish move through water, however they move, there is no end to the water. When birds fly through the sky, however they fly, there is no end to the sky. Fish and birds have never once, since antiquity, run out of water or run out of sky. When their need for water or sky is great, its availability is great, and when their need for water or sky is small, its availability is small. Acting this way, fish and birds realize their limitations yet at every moment somersault freely through their realm; but if a bird leaves the sky it will die at once, and if a fish leaves the water it will die at once. So we understand that water is life and that sky is life. Birds are life, and fish are life. It may also be that life is birds and that life is fish.   
The experience of our own existence is also like this. If a bird or a fish decided to move through the water or the sky only after getting to the end of water or utterly penetrating the sky, it would never find its way or its place in the water or sky. When we have found our own place in our own realm, we have arrived at potential. When we maintain our own true way, our action is potential itself.  
Our own way and our own place are neither great nor small; they are neither subjective nor objective; they have not existed in the past nor do they arise in the present; they are just as they are. In maintaining our own true way and abiding in our own place, to consider one thing is to explore only that one thing, and to perform one action is to fully participate in that one action. In this state, we exist in our own space and practice our own way, and awareness of ourselves is not conspicuous. The reason this is so is that our own thoughts and actions and the realization of potential appear together and are experienced together.   
Do not assume that we can be conscious of potential, or that potential can be recognized by the intellect. The experience of potential is not necessarily a cognitive realization.  
Realization is the state of ambiguity itself [kahitsu -- how can it be convulsively decided that]
Dogen


user16635: There's a quote from the Daoist philosopher Zhuangzi that reads (my phrasing):

Call those people whom the universe aids 'the favored'. Those who
  reach for that state through learning seek what learning cannot grasp.
  Those who reach for that state through effort seek what effort cannot
  achieve. Those who reach for that state through reason seek what
  reason cannot fathom. The favored know to stop reaching where reaching
  is pointless. Those who do not, break on the lathe of heaven.

Uncertainty is a product of the mind: it is a solution to a problem of partial knowledge in complex contexts; an attitude in which we measure and calculate with what we do not know as well as with what we do know. It's perfectly normal and natural, and when cultivated it's a powerful intellectual tool; every philosopher, thinker, scientist, and academic builds a close relationship with uncertainty, at least within their own fields.
In emptiness there is no uncertainty, because the active mind — the part of the mind that reasons, anticipates, plans, seeks alternatives, etc — is put to rest. It's like floating in a boat in the middle of a lake, where questions that might provoke uncertainty — e.g., "Is it better to float here, or should I float over there? — are completely irrelevant. 
Of course, in emptiness there is no certainty, either.  Emptiness transcends dualisms...
Certainty is authentic: it is natural for us to be certain of what we believe we know. Uncertainty is honest and conscientious: it keeps us from the pitfalls of dogmatism and zealousness. We need both, until we reach that state where we need neither. Just don't cling to them.

user-1: Something more everyday (less esoteric) for you: Dogen's wholehearted way

The concentrated endeavor of the way I am speaking of allows all
  things to come forth in realization to practice going beyond in the
  path of letting go. Passing through the barrier [of dualism] and
  dropping off limitations in this way, how could you be hindered by
  nodes in bamboo or knots in wood [concepts and theories]?

You need certainty in what you are doing. So you need conviction in right view, if you're practicing in Theravada Buddhism. But you can practice zazen with conviction only in zazen (though quite what that amounts to I'm not so sure).
So don't worry too much! You're in a good place if you can drop -- all -- the rest of it.

13375: <p>For purposes of this question I define “uncertainty” as a willingness to entertain doubt or acknowledge incomplete knowledge with regards to the truth of the matter about what one knows of a particular question of subject. And I define “the truth of the matter” as an objective fact about some aspect of reality which is independent of observer or context and is not contingent in any way.</p>

<p>For a long while I have regarded myself as unusually capable or comfortable with uncertainty. Having a general willingness to see the gray in every question and to acknowledge my own incomplete knowledge. To see and entertain the viewpoints of others and to grant that my own viewpoint is not certain. A general comfortability with complexity that is above average. And this is something I prided myself in thinking of as beneficial.</p>

<p>However, I recently realized that a lot of what I define as “uncertainty” presupposes an objective fact of the matter that is not contingent. And that it handcuffs me at times in that I can be of two, three, or more minds about something and unsure of the proper course to take.</p>

<p>Moreover, it occurred to me that this is not compatible with the doctrine of emptiness which I understand quite clearly as saying that for every conception that I have... it is not undergirded by a genuine non-contingent fact of the matter.</p>

<p>So with that...</p>

<p>Is uncertainty as defined above incompatible with emptiness?</p>

<p>If so, how? If so, what repercussions can be seen as occurring with this misunderstanding? What is an appropriate definition of uncertainty or one that is compatible with emptiness or how things really exist?</p>

<p>If not, why not? Where is the error in my thinking?</p>

<p>A question that might be related, but different is <a href="https://buddhism.stackexchange.com/questions/35766/is-lack-of-doubt-a-form-of-self-cherishing">Is lack of doubt a form of self-cherishing?</a></p>
 17655: <blockquote>
  <p><strong>Case 5 of the Mumonkan</strong><br />
  Kyõgen's "Man up in a Tree"              </p>
  
  <p>Kyõgen Oshõ said, "It is like a man up in a tree hanging from a branch
  with his mouth; his hands grasp no bough, his feet rest on no limb.</p>
  
  <p>Someone appears under the tree and asks him, 'What is the meaning of
  Bodhidharma's coming from the West?' If he does not answer, he fails
  to respond to the question. If he does answer, he will lose his life.</p>
  
  <p>What would you do in such a situation?"</p>
  
  <p>Mumon's Comment</p>
  
  <p>Even if your eloquence flows like a river, it is of no avail.</p>
  
  <p>Though you can expound the whole of Buddhist literature, it is of no
  use.</p>
  
  <p>If you solve this problem, you will give life to the way that has been
  dead until this moment and destroy the way that has been alive up to
  now.</p>
  
  <p>Otherwise you must wait for Maitreya Buddha and ask him.</p>
  
  <p>Mumon's Verse</p>
  
  <p>Kyõgen is truly thoughtless;<br />
  His vice and poison are endless.<br />
  He stops up the mouths of the monks,<br />
  And devil's eyes sprout from their bodies.<br /></p>
</blockquote>

<p>So this part of your question struck me:</p>

<blockquote>
  <p>For a long while I have regarded myself as unusually capable or
  comfortable with uncertainty. Having a general willingness to see the
  gray in every question and to acknowledge my own incomplete knowledge.
  To see and entertain the viewpoints of others and to grant that my own
  viewpoint is not certain. A general comfortability with complexity
  that is above average. And this is something I prided myself in
  thinking of as beneficial.</p>
</blockquote>

<p>I can't help but wonder if you've ever been truly uncertain.  Every shade of gray you see, every conflicting idea, is just another manifestation of certainty.  You can hold it in your mind, consider its merits, and weigh its value against what you already know.  Nothing here is really uncertain as all that you take to be uncertainty depends on preexisting conditions.  Every novel idea is just showing you what you already know albeit from a different point of view.  </p>

<p>What answer can you hope to hear when all of the Buddhas of past, present, and future have hung their mouths on the wall?  What words will save your life when you are hanging from a branch by your teeth?</p>

<p>Real doubt leaves us dumbfounded.  There is nothing comfortable about it.  The kind of doubt that stops up your head with cotton and hits you in the forehead like an unseen cabinet in a dark room is the kind of doubt that is truly productive.  There are no edges to hold onto.  Your previous ways of engaging the world won't help you move real doubt a single inch.  In that doubt, we are helpless and begging for our life.  We are desperate and unsure of which way to turn.  In the midst of such great doubt, we are also completely empty.</p>

<p>To see doubt is to see emptiness.  To see emptiness, we have to begin with doubt.  With faith and determination, both can resolve into wisdom. Only on the other side of great doubt can we hope to learn anything new.     </p>
 43: <blockquote>
  <p>When fish move through water, however they move, there is no end to the water. When birds fly through the sky, however they fly, there is no end to the sky. Fish and birds have never once, since antiquity, run out of water or run out of sky. When their need for water or sky is great, its availability is great, and when their need for water or sky is small, its availability is small. Acting this way, fish and birds realize their limitations yet at every moment somersault freely through their realm; but if a bird leaves the sky it will die at once, and if a fish leaves the water it will die at once. So we understand that water is life and that sky is life. Birds are life, and fish are life. It may also be that life is birds and that life is fish.   </p>
  
  <p>The experience of our own existence is also like this. If a bird or a fish decided to move through the water or the sky only after getting to the end of water or utterly penetrating the sky, it would never find its way or its place in the water or sky. When we have found our own place in our own realm, we have arrived at potential. When we maintain our own true way, our action is potential itself.  </p>
  
  <p>Our own way and our own place are neither great nor small; they are neither subjective nor objective; they have not existed in the past nor do they arise in the present; they are just as they are. In maintaining our own true way and abiding in our own place, to consider one thing is to explore only that one thing, and to perform one action is to fully participate in that one action. In this state, we exist in our own space and practice our own way, and awareness of ourselves is not conspicuous. The reason this is so is that our own thoughts and actions and the realization of potential appear together and are experienced together.   </p>
  
  <p>Do not assume that we can be conscious of potential, or that potential can be recognized by the intellect. The experience of potential is not necessarily a cognitive realization.  </p>
  
  <p><strong>Realization is the state of ambiguity itself</strong> [kahitsu -- how can it be convulsively decided that]</p>
  
  <p>Dogen</p>
</blockquote>
 16635: <p>There's a quote from the Daoist philosopher Zhuangzi that reads (my phrasing):</p>

<blockquote>
  <p>Call those people whom the universe aids 'the favored'. Those who
  reach for that state through learning seek what learning cannot grasp.
  Those who reach for that state through effort seek what effort cannot
  achieve. Those who reach for that state through reason seek what
  reason cannot fathom. The favored know to stop reaching where reaching
  is pointless. Those who do not, break on the lathe of heaven.</p>
</blockquote>

<p>Uncertainty is a product of the mind: it is a solution to a problem of partial knowledge in complex contexts; an attitude in which we measure and calculate with what we do <em>not</em> know as well as with what we <em>do</em> know. It's perfectly normal and natural, and when cultivated it's a powerful intellectual tool; every philosopher, thinker, scientist, and academic builds a close relationship with uncertainty, at least within their own fields.</p>

<p>In emptiness there is no uncertainty, because the active mind — the part of the mind that reasons, anticipates, plans, seeks alternatives, etc — is put to rest. It's like floating in a boat in the middle of a lake, where questions that might provoke uncertainty — e.g., "Is it better to float <em>here</em>, or should I float over <em>there</em>? — are completely irrelevant. </p>

<p>Of course, in emptiness there is no certainty, either.  Emptiness transcends dualisms...</p>

<p>Certainty is authentic: it is natural for us to be certain of what we believe we know. Uncertainty is honest and conscientious: it keeps us from the pitfalls of dogmatism and zealousness. We need both, until we reach that state where we need neither. Just don't cling to them.</p>
 -1: <p>Something more everyday (less esoteric) for you: Dogen's <em><a href="https://villagezendo.org/bendowa-on-the-endeavor-of-the-way/" rel="nofollow noreferrer">wholehearted way</a></em></p>

<blockquote>
  <p>The concentrated endeavor of the way I am speaking of allows all
  things to come forth in realization to practice going beyond in the
  path of letting go. Passing through the barrier [of dualism] and
  dropping off limitations in this way, how could you be hindered by
  nodes in bamboo or knots in wood [concepts and theories]?</p>
</blockquote>

<p>You need certainty in what you are doing. So you need conviction in right view, if you're practicing in Theravada Buddhism. But you can practice zazen with conviction only in zazen (though quite what that amounts to I'm not so sure).</p>

<p>So don't worry too much! You're in a good place if you can drop -- all -- the rest of it.</p>
