You wrote: "A point that would clear up the author's confusion is to acknowledge that Our Lord isn't really present everywhere."

The author isn't "confused"...  and it would be nice if you could comment without tossing out the "h" word toward those with whom you disagree.   If perhaps you don't recognize the presence of our Lord in your own life,  that would be your problem.   The religious leaders of Jesus' day were blind to his presence among them too.   He continues present among us in all times and places.

Where can I go from Your Spirit?
Or where can I flee from Your presence?
If I ascend to heaven, You are there;
If I make my bed in Sheol, behold, You are there.
If I take the wings of the dawn,
If I dwell in the remotest part of the sea,
Even there Your hand will lead me,
And Your right hand will lay hold of me.
Ps. 139