The Emperor took the place of a character referred to as "Daisy" in Early Access. Daisy was very likely to have been The Absolute and, seemingly, Orpheus in a sort of 'devil and angel on your shoulder' situation. Daisy came to each origin character as their own unique person (Vlaakith, Cazador, Mystra, etc.) and tempted them to take the tadpole powers. Therefore, it's likely that siding against the Absolute and facing your nightmares/beloved atop the Elder Brain was likely a big part of the climax from early in the development process. When Daisy was scrapped very late in development, and the Emperor put in their place with a drastically different motivation and storyline, Larian was still too married to the concept of a dream visitor and an epic confrontation with them.