I think the inconsistencies in the main plot are not due to the emperor's characterization, but due to his role. My guess is that he was supposed to be the final antagonist, the mind flayer depicted on the stone mural, and this was how the original final battle was supposed to be like. Raphael's warning, that the emperor was only using the party to get to the elder brain, and the companions could betray you (which was hinted at in EA) was true in this context. But since Larian rewrote the emperor to take the place of the dream person, the main plot ended up nonsensical in places. Now this scene only takes place when you side with the Orpheus, and the emperor's "I know your dreams and weaknesses" speech doesn't even make sense anymore, because the dream person is no longer tailored to the characters, just the same guardian for everyone.
Disregarding Stevelin's unfounded "celestial chess game" theory, they do bring up an interesting point relating to something in the OPs post, specifically about how the Emperor may scold us, but he never tries to dominate us when we do something like go to the creche. Can he actually do that?
Well, if he could, then he would have done so in the ending when the player sides with the Orpheus. Since at this point he has nothing to lose. But in the EA, the original dream person was not able to control the protagonist either.
Imo the emperor's powers are another inconsistency cause by the rewrite; in his memories Stelmane was seen fighting his mind control, yet he subdues Orpheus, who is capable of withstanding an elder brain, with ease. I think this is because originally the emperor was planned to be powerful enough to control both the illithid army and the elder brain himself, perhaps with the netherese relics. So now the writing flip-flops between just another renegade illithid, and possible ruler of illithid empire.
