This is still downstream of his autism. One of the common attributes of people on the spectrum is that they struggle immensely in terms of having a theory of mind of other individuals. Basically all human interaction and interpretation of that interaction is grounded in self-reference. TLDR as a default he (probably) has a hard time thinking of anyone other than himself as "human beings" in the way you mean it. I imagine w/ women it's doubly hard for RMS, because he has no experience as a woman that he could bring to the table.
I understand it is harder for him than for other people to be nice to others, but he is intelligent enough to work around his own limitations. If he's not, then, again, he will hurt a lot of people and should reconsider his role with the FSF.
This isn't about not understanding social cues or lacking intuitive empathy, this is about actively choosing to ignore victims telling you what you're doing to them because your position allows you to get away with it.
This isn't the first time I've seen autism (or the implication thereof) being used to reframe gross sexual misconduct as naïve ignorance and it's simply disgusting and insulting towards other autistics who can't read emotions and are socially awkward but understand consent.
What he did went well beyond "locker room" jokes like the Emacs virgins thing or "tonedeaf" postulating about the age of consent. The reason he didn't understand that it was wrong wasn't that he's bad at social cues, it's that he didn't think of women as human beings.