I forget the fallout of it but in Ghost in the Shell SAC Bato confronts Kusanagi on why she doesn't switch to a male cyborg for it's greater physical prowess and I think he gets put in his place. Iirc I think the conversation could have been handled better but at least it exists!

There's also the implication of her merging with the purely digital entity at the end of the original movie.

There's also theories that the Major's original meat space is so wrapped in mystery but some clues suggest AMAB.

All that to say, a lot, but not all, Ghost in the Shell series are worth some time!