Ok, so this issue is actually older than the popularization of trans discussion. This divide wasn't originally Futanari vs. Trans, it was Futanari vs. Shemale/Newhalf, and how porn/hentai sites would label and categorize them. Obviously a couple decades ago all of these terms were even more obscure and niche than they are now, so people tended to use them even more interchangeably. This effectively laid the groundwork for the confusion going on now. Things were further exacerbated when words like "tranny" and "shemale" became looked down upon, and everyone was told to stop using them, because now it's like "well shit, we have this entire TAG of porn that we have to switch over to something else, what do we do?" and so while some switched shemale over to trans, a bunch of other people said "fuck it, futa already exists and it's close enough and no one is yelling at us for saying it, so any girl with a dick is a futa"
There are other sites that kinda fix this problem by using "dick girl" as the umbrella term. Anything that presents as a woman, but has a penis, is a dick girl, and then within that category are futanari, trans, newhalf, etc. etc. and you can have your minutia there.