I agree, but I would go farther and say that Sci-Fi, Fantasy, and Western are also not genres in the same way. They don't describe the story in the way that Romance, Horror, Comedy, etc do; they merely describe the trappings.

Yeah some are genres, some are settings, and some are just the rules a universe follows

Disagree. They are genres because by and large (genres are fuzzy) they usually differ in the ways they approach knowledge, plausibility, and technology. Of course there is overlap, hybrid, etc.

This. You can't say superhero isn't a genre, then say fantasy is a genre in the same breath. I agree that many superhero stories have big problems, but one could say that's a problem with the premise of the genre.