It's because it was Quesada's idea to shake up things and to cull numbers because he had a bad interpretation of minorities and marginalization. In the early 2000s Marvel wasn't trying to push Fox into selling the rights back. Marvel wasn't in that kind of position yet. And really wouldn't be until they were bought up by Disney. Which didn't happen until 2008. Them excluding mutants from everything to push Fox into stricking a deal didn't happen until 2014.