I suspect there may have always been an Emperor, but him being the actual ruler of what's remained of the Illithid Empire, which is on its last legs. So now you get a dynamic of the Emperor setting you up to go against the Gith, Daisy being the tadpole trying to win you over to become Illithid, the Gith being your primary ally against them, but Orpheus turning out to be your Guardian in the Prism - and that setting you up against Vlaakith [or the other way around]
That makes perfect sense for a primary plot.
There is no emperor or guardian in the artbook, but there is Orpheus and Daisy.
Looks like last minute dumbing down from Larian to remove consequences from the game.
