Their race is irrelevant when it comes to being persecuted for their powers. The in-universe bigots don't hate Colossus any less than Storm. It's just that if you're going to make the whole thing a metaphor for real world minority struggles, then you should actually include more than one or two of those minorities at a time. The mutant metaphor has always been tone deaf, especially with the older comics.
As for Luke and Sam having it worse than Cyclops and Emma simply because they're black Americans.....eh, that doesn't sound right at all. Scott and Emma have miserable, fucked up lives.