Western, primarily American, liberals are too wrapped up in increasingly bizarre and complicated gender ideology to grasp that the Japanese might just have their own deep-seated concepts of gender and identity.
1) We have very different ideas about male femininity in the West. America, in particular. What's perceived as faggy in America isn't necessarily the case in Japan. Pretty and what we'd call "effeminate" guys actually get pussy like it's their full time job. Shit, with host bars, it kind of is their job sometimes.
2) Otokonoko is a thriving subculture in Japan. Literally means "male daughter". Basically, guys who just wanna look cute and girly without trooning out. Most of which are straight and "straight". Which enrages the troon. Especially since your average nip who crossdresses as a hobby will pass better than just about any tranny in America.
3) Japan still makes media that shits on trannies, so they perceive every actually trans character as being somehow offensive. So, as a result, they simply ignore actual trans character and latch onto femboys and project their own insecurities on them. It's the same reason blacks always keep redrawing anime characters with dreadlocks or bitching about a lack of nigs in Rurouni Kenshin or whatever.
The Halo Effect is a hell of a psychological phenomenon.
Naoto is a great litmus test to see if the player is capable of reading. She just straight up exposits that she doesn't want to be a man, but treated with respect in her chosen profession. Not to mention that she explicitly likes when the player appreciates her femininity, and the ending cutscene in Golden has her dressing more feminine, and growing her hair out.
If someone's so up their ass about troonshit that they come away thinking Naoto is supposed to be trans, they are insane.
People who don't get Naoto or Kanji's arcs are actually, literally illiterate. They both look directly at the camera
and spell out exactly what their deals are. To sit down and play the game from start to finish and actually think Kanji is a fag or that Naoto would mean willfully misinterpreting the game. Kanji's whole issue is about how he's fearful he'll be
perceived as faggy. He's athletic and in shape (Which is more of a gay stereotype in Japan than being a crossdresser) Which is another theme people don't pick up on a lot of the time. The TV theming goes two ways. Lenses and cameras can distort an image, so that's why his Shadow is all hard gay.
Doubly so for Naoto. It's not a trans thing. It's a "women in the workplace" thing.
American trannies and LGBT types are incapable of even doing a simple google search when it comes to Japanese cultural stuff, despite consuming enough anime to make them troon out. If it's not negro rap or heckin' oppressed muzzies, they don't bother to try and understand