I think it makes a lot of sense. Of course there are differences between men and women. This has been used to deny women entrance to universities, to take out loans, to own property, vote, participate in politics, make laws, start companies, become scientists and doctors, run marathons, and make many substantial decisions about their lives. If these differences weren't historically used as justification to deny people the ability to have control over their lives, then yes it would be easier to talk about them. Given the reality of how "focusing on differences" turns out for certain groups, it makes sense why people push for a more complete conversation than just Male != Female.
I have never spoken to a single person who flat out denies that biological differences and preferences exist between men and women. I think it is largely an uncharitable summary of the view that "Men and women aren't as different as society imposes through socialization." I don't think that most feminists claim that men and women have no differences. I also don't think it is politically incorrect to acknowledge that men and women are different and may have different preferences, as long as it is not used in the context to dismiss valid concerns about how women and men are treated socially, politically, and economically.