I wanted to say that it's hard to define exactly what is or isn't sci-fi. Really I'm just a sci-fi enjoyer and am not qualified to say what is or isn't sci-fi :D
Kryptonite for me is clearly a magic rock but in the movie it is in the realm of their science. Also there was a movie where the existence of superman led to a lot of questioning on its implications in defense politics so it could fit some part of your definition I guess?
So like superman is science-based and X-Men is also you're right and it does clearly ask what it means to be human when there are augmented humans now. So clearly more sci-fi than superman.
But films can be both sci-fi and fantasy. It feels like a sliding rule depending on the amount the universe is based on hardcore science. On the DNA subject, Gattaca is not fantasy but X-Men is.
To me it feels similar to the debate about "hard magic" universes like Eragon (where every spell has a physical toll on the user, or other book series where the magic is really detailed in-universe and only mastered by experts who have to study their whole life for even a basic spell) and "soft magic" like Harry Potter where everyone can cast crucifixion spells at the speed of an automatic rifle (I'm slightly exaggerating).