If it's any small consolation, Ruka's VN endingSteins;Gate 10 first couple minutes
Well... that's really awkward. And is this just the show, or does Japan in general have like no concept of transsexualism?
is based on Okabe not wanting to physically deny Ruka's gender, and prioritizing that highly enough that he gives up on saving the world. That does mean its a Bad End though, so... Eh
Japan does seem to be at best America-level when it comes to these kinds of things. Of course, you get exceptional shows like Wandering Son on rare occasions.
Also, the fact that no one else has mentioned it yet kind of makes me think that I'm just misinterpreting things (which would be rather awkward), but this season's Tamako Market has Kaoru. I don't remember any specific reference to gender, but I would have taken her(? now I'm questioning it) to be female instantly if not for Daisuke Ono's voice. I like to treat examples like that as progressive if nothing else shows I'm wrong - or even sometimes when things do, like with the Pokemon BW2 female protagonist.