My scenario doesn't preclude this from being true. It could very easily be established that mutants would be an eventual evolutionary inevitability; the proposed experiments could just have prematurely jump started their proliferation.
I completely agree that HOX/POX is a much bigger success than UXM. I think this approach would basically use very specific pieces of the UXM origin as a means to get the MCU Mutants to a place where they can quickly and dove tail into more traditional stories and takes on the characters. More or less a "Use what works, Lose what doesn't" approach.
I'm not sure that it necessarily has to, given the reasons above.
Oh your totally right about the continuity; I just find overthinking it half the fun
I'm under no illusions that Marvel or Feige care about anything beyond surface level continuity nods.
They were absolutely successful (at least until Apocalypse), but I strongly suspect Marvel will want to have their own interpretation of the franchise. Which means holding onto the fans made by the previous films, but not emulating what came before. It just seems using the "pre established" characters very sparingly (at least initially) would allow them to play to their base while still freeing them up creatively to use newer characters and stories.
I agree that the civil rights analogy as it was initially envisioned has not aged as well as some would like. I do think that the social movements regarding mutants rights need to happen for anything like HOX/POX to believably occur. Jumping right to the nation state point (or even getting there in short order) will make the mutants more like the Inhumans or Eternals. I just don't think Marvel would prioritize a take on mutants that makes them less of a perceived social collective within society and more of an external, hidden and separate society. They could, I just don't think they want to use the franchise for that take when they have other, better fitting options like the ones I said earlier.