Maybe that's a nitpick, but I would say it's fundamentally impossible to mathematically prove anything at all about a physical system. You have to assume some model to do the proof and have no way of ever "proving" (what would that even mean?) that model.
I guess you're referring to the fact that verification and formal methods are used in hardware more often than software. This is due to commercial reasons: you can't just reprogram a million chips once they leave your fab.
What you mean is that it's practically infeasible to verify every program behaviour we're interested in. That's probably true for large enough programs, but it doesn't mean we can prove nothing about them.
I don’t think this is true, something as “trivial” as halting already can’t be proven in the general case.
Of course, what you are saying about “stronger systems can prove the answers to the questions of the whether the machines from larger sets, halt” is also true, I just, wouldn’t describe this as “the halting problem”, even though they are I guess basically equivalent.
A typical theory says:
For all x:A, P x
In other words, given any x (from an infinite set A) P x is true. Where P is a proposition.
You typically prove it using straightforward induction/recursion.
And the number of possible states increase so fast that you might as well think of it as infinite.
Gödell showed there are algorithms that we cannot prove, but he did that with self referencing algorithms which we rarely use.
Still, you can’t even in theory prove every interesting property about any problem/algorithm.
It also isn't clear that the machines itself actually do what they say, though hardware is a lot more likely to be mathematically proven.