1. Mutants are genetically a different race of humans.

2. The X-Men have almost always been a metaphor for racial conflicts.(and just about any minority group really.) 90% of their storylines involve mutants being attacked by angry mobs, enslaved, put in concentration camps, and just plain massacred.

That’s not even subtext, that’s the main theme.

I don’t think you’re read that many X-men comics.

^I’m just now really diving into the X-Men comics (starting with the Uncanny 1963 comics) due to X-Men 97 reawakening my passion for the X-Men but even if one just watched the og animated series and the pre-Disney X-Men shows these points are thoroughly covered. As you said, this is definitely not a “Disney started this” situation.