Why is making a general statement too vague a problem? I think the point of the X-Men and "otherness" is to make people relate despite race, sexuality, religion, disability, etc.. or whatever minority you identify with and relate to the X-Men for that reason. To reach across gaps and form common ground. I think the reason why many people related to the X-Men and liked them is because it could apply to lots of different minorities groups, some which we don't really always recognize or talk about as much.
Heck I'm part of two (race, sexuality) and I've never felt like the message was lacking. The only thing I felt was lacking was the franchise taking it's own metaphorical advice and portraying minorities in important positions in terms of story, which is still an issue at times but has gotten better, a bit slowly.
Anyway just because someone addresses real life racism in another book, doesn't mean the points about tribalism or "otherness" goes away in different books or makes it redundant. There are nuances and history to each minority that makes their experience different, while an umbrella category like the X-Men serve as a unifying metaphor for themes that probably might be too radical or ignored in separate mediums.
Since this is Disney, they are going to play this as safe as possible, using a metaphor lets them address things indirectly without making the comparisons too heavy-handed. The execution will matter regardless of where it's coming from, whether a film like Ms Marvel or the X-Men. Ms Marvel doesn't represent all minorities and none of those movies should get the benchmark as having exclusive coverage of the ideas of discrimination, it's affects lots of people and in lots of different ways, so I don't see a problem.