Ceremorphosis is a tricky thing, I'm not fully sure what to believe in that regard.
I’m not 100% either, but as I understand it, “free” mind flayers like the emperor are not actually their old selves, just a grown brain parasite that has inherited the original person’s memories and personality. It’s mimicry and the original person is dead. Withers and the game in general are very clear about ceremorphosis being soul death, and in fact now that I think of it the only ones in the game who try to contradict this are themselves illithid.
