I always thought, the emperor did something to him (like tadpoling him for example, since he seems to have a collection of tadpoles on him), which is, why he would be able to transform.
Personally, I would have preferred Omeluum being there, if we freed him, to become our local friendly mindflayer.
Or at least have Lae'zel to volunteer. I mean, sorry, but I don't know Orpheus, why should I take the hit for him? SHe on the other hand sees him as githyanki Jesus.
I love the game, I'm still palying it after five years, but I don't like this forced decision honestly. I thought, the reason we meet and save Omeluum is, that he can help us with the brain. As is, you can either go with the emperor, wo manipulated you through the whole game or sacrifice yourself, Orpheus or Karlach. So I normally go with Orpheus.
In my headcanon, we recruit Omeluum and no one has to become a mindflayer. And if I ever manage to bring Lavi story to paper, this is how it will go down.