Should I list my degrees chronologically, or in order of relevance in my CV? Say that I have achieved a Masters degree in Physics, then a Masters degree in Mathematics. Then for a couple of years, I focused on different fields. I have had placements related to agriculture and botany, as well as taken online courses in Machine Learning. After careful consideration I decided want to pursue a PhD in Physics and so I am preparing for applications.

Normally CV's are written in (reverse) chronological order, most recent experiences first. However, my path is not straightforward, and so I am confronted with a choice.

On the one hand, since I have been told that a CV could be glanced at in less than 10s, I would want to put the most relevant (and prestigious) elements first. On the other hand, I am required to have those degrees to simply be eligible in those courses, and to provide the relevant certificates. This makes me want to keep the CV in reverse chronological order, for the sake of clarity and simplicity.

In the motivation letter / note of research interests I can also briefly explain my path, highlight my relevant experience and thus perhaps reduce the need of highlighting it in the CV.
I would stick to the standard listing. As you say, the reader wants to spend only 10 seconds, so don't write it in a way that might confuse them. If you list a lower ranked degree before a higher ranked one, they may stop reading at what they imagine the end. 

In general it probably isn't good to get too clever in lists of things. Be clever in your letter and interviews.