i think if you think ruka's arc in steins;gate is transphobic you have poor media literacy skills, are blinded by insecurity or have a really trivial definition of transphobia. okabe's whole fucking arc with her is going from being dismissive of her to not only seeing her as a girl but someone he could absolutely have romantic interest in. this kind of arc of not really connecting or respecting the other people around him to taking them seriously is a constant theme in the show with all of the girls that okabe interacts with in the show. you'd have a better argument that the rest of the gendered stuff in the show carries more transphobic baggage than this. ig there is an option that you could just be unaware that japanese doesnt have second person pronouns and are confused by some shitty subs sending mixed messages about that conclusion but there's still not really a way to miss him saying he promises to never forget her as a girl no matter what world line they're in