tbh I’m not too worried about Bill.
I mean, Nardole lost his entire body and he’s completely fine, apart from being made of parts that the Doctor got cheap.
Plus, the Mondassians clearly haven’t figured out how to delete emotions yet, as all they can do is mute the voice-boxes to keep the patients quiet.
So I think Bill is going to be just fine. Somewhat cyber-fied, but still with a human brain and human emotions and probably a far longer life-span than a normal human being would have (btw I love that new trend in Doctor Who of “revive your gays and make them functionally immortal”. Well, I say new. Jack Harkness did it first. I wonder how many of the other immortals he met).
Also, Bill had been sort of okay with the idea of travelling the universe as a puddle, with another puddle. She’ll probably be fine with being not 100% human.