So I looked into this (since Ramachandran's done some really good and interesting work on phantom limbs, synasthesia, neurological pain/pain without physical cause etc.), and... well.
This was the first thing that popped up.
Tl;dr the journal he's published his trans research in has a crappy reputation (it's previously hosted papers denying AIDS exists, and claiming primrose oil can cure diseases), it's not really peer reviewed (which is a Huge no-no in academia), and most damning of all, Ramachandran is on the editor's board (which is like... the #1 thing to look for if you're like "this paper seems crap and weird, why's it getting published". Corruption is why lmao).
Also, it's pretty easy to induce phantom limbs or similar sensations in people, with simple tricks or meditation techniques. I could induce a phantom penis in myself (if, for some godforsaken reason, I wanted to); doesn't mean I'm a true and honest man, it'd just mean I'd lightly broken my brain lmao.