Yes and no. Certainly these are concepts that we've created, but the question is, do they have some kind of corresponding elements in whatever reality is?

This seems to be more or less an argument from incredulity. It seems unlikely to you that we'd be able to understand reality, so you're just assuming that we don't. And then it seems amazing to you that our theories work at all, because it's "overwhelmingly obvious" that they don't bear any relation to what the universe is really like. I'm saying, maybe it's not that amazing. Maybe the reason our theories work so spectacularly well is that they do correspond to reality. Not perfectly, of course. But neither are they completely unrelated.

This is the attitude that I find strange. You seem to be assuming a priori that the universe is incomprehensible. So when theory does well, and the universe looks like maybe it is comprehensible after all, you instead hold to your postulate and insist, no, those are just models, we don't understand reality at all. The universe is not really filled with baryons and leptons and photons that interact according to certain rules. Instead, it must instead be something that we cannot ever hope to understand that for some odd (and presumably equally incomprehensible) reason happens to behave just like it were made of baryons and leptons and so forth.

I'm certainly not suggesting that we have everything figured out, and I'd even acknowledge that maybe we never will. But you seem to be taking the extreme point that reality is completely unknowable, and I don't think you actually have any evidence for that apart from your own intuition.

It is sad that we've lost so much of that. And I wouldn't suggest that we're intrinsically smarter than any of those people (actually, on average we're probably not nearly as smart as the ones whose writings have actually survived, since their ideas were the ones later people thought were worth copying down). On the other hand, they hadn't really come up with the idea of actually testing their ideas to see if they worked. The ideas seemed "reasonable", but as we've discovered, being reasonable isn't a good way to tell if that's the way things actually work.

Let's look closely at some of these more recent examples, though. Once we thought atoms were the smallest components of matter, and that they came in a large number of varieties. Later we realized that in fact, they have internal structure. Many of the properties of various types of atoms (that up until then could only be determined experimentally) could actually be deduced from theory. But even though we now know that atoms are composite entities, does that mean taht it no longer makes sense to talk about atoms? Or that many of the things that we had figured out about how atoms behave wer suddenly no longer true? No, that's not the case. So then we discover that the protons and neutrons in the nucleus aren't fundamental either. But even with the existence of quantum chromodynamics, is it meaningless now to talk about protons? Again, no. For that matter, with the development of quark theory, that changed what we (think we) know about protons quite a bit, but atoms, not so much. Moreover, I'd be willing to make a Hawking-like bet that any new theory we develop will still have elements in it that correspond to protons, electrons, and so forth. So, unless you want to deny the existence of objective reality altogether, I'd actualyl say that protons are real things. To be precise, there is an element of reality that corresponds to what we call protons. Of course it's almost certain that we don't understand them fully. But I don't think it's realistic to think that in 500 years our descendents might be laughing, "can you believe it, they believed in protons!" in the same way we might laugh about phlogiston.

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Conserve energy. Commute with the Hamiltonian.