I mean, it is kind of getting into the weeds of Mega Man lore (which I'm sure someone who has written a robot master field guide or two would never consider), but I always got the impression that including "humans" in any Mega Man X game would be like... horrifying? Like, most people would not react well to knowing that their species is basically little more than ants in this conflict between shiny robot men and mechanical mammoths that spew fire. And I feel like this was all but confirmed in Maverick Hunter X, where it was like, "Here's Dr. Cain! Watch him get exploded! .... Okay, let us never revisit this again!"
Like, if they want to maintain the "what am I fighting for!" tone of the Mega Man X series, they kind of have to ignore the "world", as it quickly becomes a situation similar to (I think) Don Rosa's opinion on never discussing the parents of Huey, Dewey, and Louie: there is no explanation for what happened there after years of stories without it being an incredible downer tale of children being orphaned or abandoned (or both). Is there a possible explanation that isn't tonally inconsistent with tales of daring-do ducks? Contemporary Ducktales went there, so yes, but I can understand how an author wouldn't want to take a turn in that direction in an already "experimental" side story.
Basically, what I'm saying is that the Mega Man franchise is just centuries of war that resulted from two old dudes arguing over the purpose of cleaning robots, so I don't fault them for not exploring what that (horrible) world would actually look like.
.........
For more information on the state of the world after a Reploid War or two, please play Nier: Automata.