Let me make a few comments from an ex mathematician (now physicist).
The first thing to understand is that the notion of "proof", namely a formal derivation with logical consistent steps to show that some statement is true, from purely theoretical grounds is not as central for physics as a science as opposed to mathematics.
Within science, specifically in physics, I would say the general view is definitely more pragmatic. Of course among all physicist you will find a whole spectrum of postures, were some will give more relevance to current theory or experiment, depending on where they themselves stand. Nonetheless, the ultimate test for a theory or a model will be experiment (that is science). So as theorists we must accept the fact that we should never confuse the model with reality. We can only produce models and they are just as good as their predictions.
Having said that we can discuss your concerns around the Schrödinger equation. As I explained this is a model of a piece (or a regime) of reality pertaining certain energy scales, lengths and time scales. As such it has been proven (verified) to work wonderfully for a specific regime, namely very small scales in length, and low energies (compared to rest masses for example). Under this view, the claim that the Schrödinger equation describes reality is just to broad and ignores the details. We know for example it breaks down at high energies (must be replaced with the Dirac equation). Alternatively, many argue that the higher the number of particles involved in your setup the closer you should be getting to the classical regime (high occupation numbers lead to classicalization...), however in the in between there is still a lot of phenomena and as physicist (some) we care about using what we would call the "current fundamental laws" to build up models that effectively describe the setup at hand. Thus, all the already mentioned, statistical mechanics, DFT, mean field treatments and so on, to be able to describe larger and larger numbers of particles.
Our job is precisely to keep testing and testing and testing... If we find that something disagrees with the Schrödinger equation, we change it, that is science. And that is what has been done in time. We know today that QM is way more than just the Schrödinger equation, its essence relies on non-commutativity of observables. This precise idea has been extended to a wider regime, such as high energy physics, also with excellent agreement. So objectively I can say, QM is the most fundamental description of the smallest scales of length we currently have.
I hope I have been objective enough.
P.D. By the way, modelling things fully classically with Newton's laws and the corresponding equations, faces the same issues when dealing with a large number of particles, so one goes again to effective theories derived from some averaging procedure. However, there is still little doubt that Newton's laws are correct (they predict up to our current experimental precision) at describing the mechanics of our daily life.