There is a lot of food for thought in your comments, and I don't have time to answer all of them in one go. This is just the first of several replies and I will address the rest of the issues you have raised in due course.
For now though, I just want to comment on "naturalism". I think it is unfair to criticize the term on the grounds that it does not have a clear and unique meaning. If you look at any similar philosophical term, such as even your favoured "idealism", you will find that they typically refer to a broad church of views that have a main theme in common. The term itself serves as code for this set of views and it may be used when the distinctions between the sub-varieties are not too important for the issues under discussion. Add to this the fact that FQXi essays are supposed to be pitched at a general audience, and I don't think I have been too vague in using this term.
As far as my stance is concerned, I mean two things by the term "naturalism". The first is that the results of scientific enquiry are not to be ignored when they are relevant to a philosophical enquiry. This is a fairly innocent claim of methodological naturalism, that I think is fairly mainstream in western philosophy. So, for example, an enquiry about consciousness should take into account the results of modern neuroscience. For mathematics the main implication of this brand of naturalism is that, since modern theories of physics use advanced mathematics in an indispensable way, we need to find a theory of mathematics that explains why this is so rather than leaving it as an unexplained miracle.
However, I do also adopt a stronger version of naturalism, which you may want to brand "materialism", but would more properly be called "physicalism". Here, the idea is that our best guide to what fundamentally exists in the world is physics, so I want a metaphysics that does not posit entities beyond those of physics, or at least one that does so only minimally. Note that, just as with empirical science, the implications of this view are revisable. If a scientist one day discovers reliable evidence for ESP, or is able to reliably detect "mind particles" or some such entity, then the idea that we have to explain everything in terms of what we nowadays call physical entities would have been shown to be incorrect. The point, however, is that this is a matter for science to decide, and we should not go around positing such entities purely for the purposes of our metaphysics.
As for psychology and the like, physicalism is perfectly consistent with the concept of emergence, of which the emergence of thermodynamics from statistical mechanics is a prime example. The emergence of consciousness, human psychology, sociology, etc. is supposed to be explained in a similar way, but since they are much more complex than thermodynamics, we cannot boil this down to a few simple equations and relationships. Nevertheless, we have no good evidence that they require positing any new fundamental entities beyond those of physics.
You are right that I do not enter into a defense of naturalism or physicalism in my essay. The starting point is to assume these things as premises and to see what theories of mathematics they are compatible with. That is why "platonism falls afoul of naturalism" is appropriate in the context of this essay. I do think naturalism and physicalism are fairly mainstream positions in philosophy of science, so I don't think it is inappropriate to argue from them. However, I agree with you that, in a broader context, these notions require a defense. Getting into the general debate would take us into deep waters that are probably not too relevant for the philosophy of mathematics specifically. However, it is important for naturalists to come up with a viable theory of mathematics. If we cannot do this, as you seem to think we cannot, then that means that we would have to abandon naturalism, at least for mathematics, so this is an important issue we should debate further.
Finally, regarding the comparison of my essay to Lee Smolin's, you say I have been vague but I don't think so. Lee thinks that, for physics, we can get away with number, geometry, and maybe a few other things. For him, these things are straightforwardly "real" and the rest of mathematics just a formal game. Lee's views are actually quite close to those of Quine on this issue. Both of them think that it is possible to ring-fence some areas of mathematics as the "physical" ones, and not be too bothered with the rest. I do not agree with this position as I think that more advanced mathematics is truly indispensable for modern physics and it leaves the applicability of such mathematics to physics a total mystery.
In contrast, for me, there is no distinction to be made between "physical mathematics" and the rest of mathematics. ALL of mathematics is derived from the natural world, and ALL of it is real in exactly the same sense. I hope this is a clear enough statement of my main thesis and how it differs from Lee's. There are, of course, subtleties. I am at least partially a pragmatist about scientific truth, so when I call something "real", what I really mean is that it is useful, indispensable, etc. to the entities who practice science. Therefore, to defend the idea that mathematics is real I have to explain how it is constructed and why it is useful, rather than trying to locate it explicitly in the physical world as a nominalist would. This applies to all of mathematics, including the basic concepts like numbers as well as more advanced branches of mathematics.
I'll get into some of your more specific criticisms later, but I hope I have at least clarified my main position.