Dear Tim Maudlin,
I will comment mainly on the first part of your essay. (The second part of the essay, in which you outline your new foundations for geometry, is interesting in it's own right, but it does not seem to address the original question as directly.)
One aspect that I liked is that you distinguish the surprise due to discovering a connection between seemingly distinct parts of mathematics from the wide applicability of mathematics to empirical sciences.
In the first part, you also think about how the world needs to be in order for the counting numbers to be relevant. You give mountains and cells as examples of concepts that are not (always) sharp enough (conceptually) for counting, and atoms as an example of a concept that is. In my view, however, the sharpness of our concepts is a matter of degree. The concept of an 'atom' is still a vague one, to some degree; hence the question of whether something is an atom or not -and whether to count something as an atom or not- may still be ambiguous in certain situations. For instance, one can imagine an electron and a proton: they will always 'feel' each other's electrical field. When, exactly, do they form a hydrogen atom? This question is also relevant in foundations of chemistry (with competing partition schemes in computational chemistry to identify 'atoms in molecules').
Viewed in this way, there are many degrees of freedom in applying mathematics to empirical findings - something which is rarely discussed in relation to the perceived effectiveness of mathematics.
Best wishes,
Sylvia Wenmackers - Essay Children of the Cosmos