Looks like, i should have not taken the bait ...
But still the Gerudo culture isn't uncommon for human culture in the real world. Just look at Saudi Arabia. You have the problem, where your gender is in the way of entering a place, so the obvious solution would be to cross-dress. Tropes also aren't bad by default, it is important, how you use them.
Again i may not be transsexual, but i never felt, that Link or anybody was punched down for the cross dressing. There is also something transcending, since it may start as a joke (which clearly is the transphobic part of it), but they game never has a punchline and eases you into liking the cross-dresing. Even the Gerudo's look through Link's disguise, don't care really and even compliment Link for his looks.
Because exploring non-binary gender isn't the focus of the story, Nintendo tries to tell. The focus in Zelda since OoT was always more centered about the interaction and synopsis between different races. It isn't overly complex, but it also doesn't try to be more. You can't fault somebody, for what they don't try to do.
Undertale's main character is also a very bland state and isn't meant to be more. Most people in the game only see him/her as "human" and his/her alienes in context of the world of monster are the center about most interaction. So it really doesn't matter for the story and the other character, which gender, skin color or anything else the main character is in the game except being human.
