I don't think anyone could reasonably argue that the attitude that men are smarter than women (or at least, better at chess) didn't exist previously, and that's why they leagues are setup this way. But it's one thing to not change existing policies rooted in sexism, and another entirely to create new policies rooted in sexism.

The former happens literally all the time, because large institutions are slow to change, and even though blatant sexism is no longer socially acceptable, it's still prevalent in peoples' heads. When the latter happens, it understandably causes more uproar, because it's an active move towards more sexist policies.

Don't get me wrong, we should absolutely get rid of gender based leagues IMO and switch to having leagues based on ability (whatever the critical ability might be for the competition in question) and call it a day - that would solve both the sexism issue and the trans issue, as there would no longer be any "unfair advantages". What genitals a person was born with - whether they kept them or not - shouldn't impact how you're allowed to compete especially in an activity like chess that has no reasonable basis for gender separation in the first place