Not to resurrect the discussion but this probably wouldn't be an issue if there were an actual umbrella term that can be used for both, so that futa can be used exclusively for futa. But at this point I think the habit of using futa for everything is already too ingrained in most popular sites like r34 so trying to come up with something new would just lead to more confusion.
I imagine this confusion started because when they first started appearing in hentai futa only had a dick on top of the vagina and no balls, so they were obviously different from traps/otokonoko, which have been a thing in Japanese culture since forever. But full-package futa were already the norm by the time it became mainstream in the West, while ball-less futa slowly faded into obscurity. I don't know much about shemale/newhalf hentai history, but I imagine it came after trap/otokonoko, and if you put them side by side with full-package futa they look indistinguishable from each other until you lift the balls.
So while the Japanese watched feminine men and hermaphrodite women go through this sort of convergent evolution, the West kinda got hit with both at the same time so most people who are attracted to one are probably not going to dislike the other or care much about the distinction, and some might not even be aware that there's supposed to be a pussy.