Hi Lev. I don't claim to be an expert in this area but the criticisms you mention don't seem convincing.
1. If you use GMT flows (e.g. level set method), you don't get "continuity" in some sense. I would have to dig around for references or examples if I wanted to be more specific but "Brakke flows" can exhibit this type of behavior. If you work with BV (or SBV) functions, varifolds or various types of (rectifiable) currents, "discontinuous" behavior can occur.
2. I'm not sure that one can model quantum mechanics very well. If your goal is a "theory of everything (in physics)," then I would start with an easy project like proving the Riemann Hypothesis. :D (What are the existing "good models" of QM? What besides probability measures, functional analysis, PDEs, etc. are involved with these models of QM? This is a vague question. One of my colleagues does QM & QC and has been a "fellow" (?) at KITP; I'll eventually try to formulate my question in a better manner.)
3. Varifolds are Radon measures on the manifold crossed (Cartesian product) with the appropriate Grassmannian. Don't people like Robert Bartnik, Tom Ilmanen, etc. (maybe Gerhard Huisken, Klaus Ecker) use GMT to study general relativity? (Maybe I should throw in Fred Almgren's "multi-valued functions" for fun.)
I don't think "basic math texts" would ever cover this stuff at a serious level. I'm not sure what you mean by "EVOLVING topology" as a concept; it sounds completely trivial. Now "evolution" is not trivial but the idea that topology changes as a parameter (e.g. time) changes is trivial.
What is evolution? Imagine the praise if the evolution of the universe turned out to be the solution of some flow problem and you identified this flow problem. Could QM be included in a "measure-theoretic" flow problem? I have no idea if this even makes sense but it reminds me of "string theory - banes - M theory" and multiverse (meta-universe, metaverse) theory.
I understand that physicists want to understand "reality" and not just some mathematical theory. If you would be so kind as to define "reality" this would help. ;D