Yeah, there should honestly be a tutorial on how permanent transformations actually are and how to remove them... maybe in 0-3?
The game is unnecessarily cryptic about it. It's basically only mentioned in one dialogue with Voice that doesn't really explain the gameplay aspect of it at all. It took me a LOT of trial and error to even discover the gem usage menu because I just thought the bottom left of the screen is your healthbar, and prior to that I had no idea what gems even do outside of being a quest item early on. I thought they were currency for some shop later at first...
As far as I know you can only undo transformations in the safezone/lobby of the game and in hotsprings during stages, by clicking the bottom left of your screen where you health is, and then holding leftclick to spend gems to undo one of your transformation effects.
Though it appears you can't do that for transformations once they become permanent... and if they're actually permanent with no way to remove them on that particular save that really sucks. So far the only way I know of to remove perm transformations is to get a bad end from another transformation, which overrides your default class once you recover from it. But that feels more like an oversight than something intentional.