A lot of these "problems" could be very easily addressed with a paragraph or two from WotC, and reminders scattered throughout the text of the core rulebooks, that the rules as written (including the fluff as written) is only a starting point: a compilation of tropes that, in the end, are merely the parts that each DM can assemble as they so desire.
Oh, wait, they already do that. But sure, make it more explicit. And explain (perhaps again and again) that the ideas presented are not fixed and absolute, but malleable.
This means that if you want your subraces and cultures to be more diverse, you--as the DM (or player, really)--can do that. And here, we'll provide some examples. But just because this diversity isn't expressed in every moment (which would be absurd and unnecessary) doesn't mean we're saying "all instances are this way."
I'm reminded of the "IMO/IMHO" crisis of earlier internet years. How many times did we see this:
Person A: Green Day sucks.
Person B: That's just your opinion.
Person A: Yeah, of course, because I said it. Everything I say is my opinion.
Person B: But you stated it as absolute fact.
Person A: But it should go without saying...OK, I'll cater to your hermeneutical needs. IMO, Green Day sucks. That is based upon my own subjective opinion, enculturation, and because I had a bad experience with pop-punk when I was a kid. Happy now?
Person B: No, because your language is aggressive and implies that if a person likes Green Day, they have bad taste.
Person A: (pulls out hair)
The point being, there's no end to this, and it is likely that Person B will never be truly pleased and always find something "problematic." Their concern is valid, but they are--imo--misplacing it through an act of concretism. So yes, I think a lot of this comes down to a variant on misplaced concreteness.
There are other solutions, however. We can recognize that fantasy races and subraces are archetypal, based on archetypes. An archetype is not the same thing as a stereotype, which is a specific, crystalized form of archetype. Meaning, an archetype is a living symbol that can express itself in different ways, while a stereotype is static and "dead."
Furthermore, they are fantasy archetypes. They aren't meant to depict real world people. But they do represent an aspect of people. If we go back to Tolkien, elves were "angelic men" - more perfect, closer to the divine, but also somewhat set in their ways and lacking the adaptive nature of humans. Orcs were "bestial men" - twisted by evil. And so on.
The nature of fantasy is that it is always simpler than real life, so will never adequately emulate the real world. Human imagination is symbolic and representative. It deals in myth, not history (and myth is not false, but a different kind of truth). When it tries to simulate in a literal manner, it gets lost in a morass of complexity and over-concreteness. Cognition, by necessity, simplifies and teases out certain elements of experience, otherwise we would be completely overwhelmed. Imagination takes the complexity of the real world and forms it into archetypal and symbolic patterns.
So my solution is that the core rulebook books simplify a bit and present an archetype, or something as close to an archetype as possible. And, more importantly, they explicitly present a game philosophy of "infinite variation and customization" and present examples within specific campaign worlds.
So the PHB would have "Elf" and maybe "High" and "Wood" elf, even "Drow," but Eberron, and the Realms, and Dark Sun, etc, would all present different variations on the form.
Again, this is pretty much what they've already done, but I think making it explicit would help recognizing that the archetypes are not stereotypes and thus not subject to the same critique that stereotypes are rightfully subject to.
