I am wondering about this and have wondered about it for a short while. Usually physics is modeled using things based off of the Real Number Line $\mathbb{R}$, which is uncountable. (E.g. we may use powers of $\mathbb{R}$, we may use $\mathbb{C}$, we may use "manifolds" which essentially glue together "warped pieces" of $\mathbb{R}^n$, etc.) But is it possible to dispense with this uncountable set, and uncountable sets in general, and still do ALL of the mathematics used in ALL physical theories which are supported by empirical evidence?
In particular, there is a type of mathematics called "constructive analysis" (a subfield of more general "constructive mathematics") and one approach to this is to jettison $\mathbb{R}$ and replace it with the sub-field of "computable real numbers", which are real numbers for which we can write a (possibly computationally intractable but not impossible) computer program to approximate to any desired $\epsilon$ of accuracy (where $\epsilon$ is a rational number). This reduces our set of real numbers to a countable set, and if we keep all our other objects computable as well, we can get a good deal of analysis done. There are some caveats -- e.g. equality is not decidable, we can only tell if two computable reals are within a given $\epsilon$, however this may not be a problem since it lines up neatly with the way empirical science works -- we can never actually prove two physical quantities are equal by empirical measurement, only that they are equal to within some $\epsilon$, namely, our measurement error. E.g. in all true honesty, we cannot say the mass of a photon is 0 -- we can only say that it is $<10^{-18}\ \mathrm{eV}$, at least, according to Wikipedia as of now. Another caveat is that bounded monotone convergence fails: we can find a bounded monotone computable sequence of computable reals which has no supremum. But despite these, like I said, you can do differentiation, integration, etc. . It also has some other interesting properties, e.g. all functions are continuous.
So with that in mind, is what I am suggesting possible? Or is there some type of math in physics that for some reason requires uncountable sets? Can we do every mathematical proof needed for physics' math to work out in these constructible, countable sets and maybe even better, with no proofs by contradiction, i.e. intuitionistic logic and no law of excluded middle?