Yeah, I'm much more used to the later status quo where everyone basically knows that mutants exist, and I agree that the metaphor(s) work better that way. (And I agree on which real minorities have the closest parallel to mutants.)

This era uses the theme of prejudice, but it's also a lot closer to their sci-fi origin story, and the combination feels a bit odd to me. Even though of course mutants had to be unknown sometime, given the premise!

And yeah, the contrast to Nightcrawler's story is really interesting; I think the parallel there makes me like this story a lot better than I would have otherwise.