I never really felt like the show was meant to be pro-tranny or even had anything to do with actual trannies. The premise is basically just "guy gets cursed and now turns into a woman every time he's splashed with water, comic mishaps ensue." He doesn't want to be a woman, he's not sexually attracted to men, and he spends most of the series trying to figure out a way to break the curse. It's just a comic device, I think you only see it as pro-tranny because of the way trannies are viewed in the US. Japan probably has some kind of stigma associated with actual trannies and fags but I don't think it's quite the same as it is here. I notice in some animes there are cross-dressing characters, but it's usually used for humor, like the male character will hit on the trap thinking it's a woman, then find out it's actually a man and be like "eew gross".
Also I don't really catch a gay vibe off Inuyasha, I think it's mostly just that a lot of anime characters tend to look the same, and male characters can sometimes be drawn as slightly effeminate looking, especially when being drawn by a woman. By that standard I think Clamp's male characters are much gayer looking.