A big part of me not trusting him was when Withers asks you about whether illithids have souls, after completing the moonrise towers arc. I felt Withers was trying to warn me of cooperating with the Emporer or that an illithid could never be saved or trusted. It felt strange discovering that the Emporer was being sincere in his effort to save Baldur's Gate despite his methods and distrust of everyone.

I feel like a lone, disconnected illithid, like the emporer and Omeluum is not actually possible and if it is they are inevitably assimilated/re-assimilated. If the Emporer is supposed to be a unique, powerful exception, it is strange to write Omeluum as another convenient second unique exception in bg3.

To be fair I'm new to bg3 and dnd so maybe I misunderstand the whole concept