Hmmm. Certainly a good rebuttal about the nature of mathematical proof. Obviously, the FAQ in question is severely simplified, so maybe an intermediate FAQ could be created? My experience has been that even mathematical undergraduates often have questions about the nature of proof in math as it's generally an aside in class and an appendix in the textbook, and that the same sort of scholastic rigor isn't applied to examining the topic like it is in science.
Okay, you raise some good points, so let me clarify.
1) Yes, mathematical physics has embraced computation and modeling, but it does so as an abductive appendage to what is primarily an inductive pursuit, and strictly speaking mathematical models of the universe aren't empirical science per se which traditionally moves from intersubjective observation of phenomena to predictive logical statements (obviously inseparable from set-theoretic and arithmetic relations) which are often infused with qualitative overtones for future predictions. Sure, they're both math in one sense, but where they come from and where they arrive at are very distinct. In this way, I would say that mathematical theories and scientific theories are entirely different beasts. Scientific theories use mathematical theories as building blocks in their proof. That's why in the popular media when famous physicists like Seth Lloyd say "the universe is a computer" or Marvin Minsky says "we may be living in a simulations", there's a lot of linguistic merit to what they say (because these are only analogies), but the statements are metaphysical, and NOT scientific. (Anyone who literally believes the universe is a computer, and we are software would have to prove the existence of hardware because information always exists in a medium, and if the medium is information, then another layer of regress!). Mathematical physics is like a calculator to the notebook of science and measurement of the world around us, and the nature of their proofs are still distinct. Simulation isn't proof of causality.
2) In regards to mathematical theories, let me say that I understand your use of the term now, and I apologize for presuming you were making the simple error I referred to. Obviously you're knowledgeable in mathematical proof. But in the sense that it tends to be used, number theory, for example, it's just a synonym for discipline. Obviously among the mathematically literate it's still used as you used it, and that's to describe an overarching collection of proofs moving in a general direction or by a theme. I do accept the point that mathematical proof is completely a function of a philosophy of math and the selection of assumptions be they axioms, postulates, or first-order predicates, etc. however, the nature of what constitutes mathematical phenomena is largely been accepted in the scientific community to be a function of human cognitive states, and therefore is embodied in the mind and explored not soley through phenomenological techniques, though they still play a role, but through correlates among neurofunction as observed by fMRI, objective measures of mathematical performance, and simple introspection. (See
https://en.wikipedia.org/wiki/Where_Mathematics_Comes_From) Note also, that I make no such claim about mathematicians who seem to violate a symmetry of using science to practice math as scientists actually practice math. (Plato has cursed the philosophy of math, in the same way Aristotle cursed science, IMO.) So, yes, they are theories, but in a way, unlike a scientific theory which is true because evidence supports it, mathematical theory is true by assumption. For example, Euclidian theory is equally as relevant as non-Euclidian theories of mathematics.
3) "What you are saying is that you can deduce elliptical orbits from Newton's Laws and certain initial conditions - as one would do with any differential equation." No, I think that's a mischaracterization, although I'm sympathetic to your simplification. Let me reiterate. Yes, one can deduce the model even with initial conditions, but in deduction by definition of the process itself, the initial conditions are irrelevant to the conclusion and therefore the deductive proof the model of the orbit can be proven, but that proof is mathematical and not scientific, where as using the deductive proof as a model to make a scientific prediction which can be verified against intersubjective measure is the scientific proof and is therefore much greater in scope. In this way, scientific theory (primarily the math deduction of a model) only plays a role in scientific practice of theory building.
Please let me know if this is clear, because the nature of mathematical and scientific proof are relevant to my pursuit of establishing a metaphysics of STEM which is rigorous. I'd certainly love rebuttals and rejoinders on where you draw the lines around mathematical proof.