Admittedly, I haven't done an Orpheus run yet but I still read this thread here and I had some thoughts on it. Please let me know if I'm wrong about how things go in a reply if you wish

I thought about this quite a bit and in the end I ended up deciding that The Emperor makes sense as a character, but their reasoning is not made explicitly clear. We learn that Vlaakith doesn't have the ability to stop the Illithids or the Grand Design, but Orpheus does and being Githyanki he understandably hates the Illithids and after the inevitable Githyanki civil war upon freeing Orpheus, their attention would inevitably be focused on the Illithids. We also learn that The Emperor escaped the grasp of an Elder Brain, not once but twice and conceivably they could do that again. It may take forever, but by "siding" with The Absolute when Orpheus is freed it gives them a chance, no matter how small, that they could do it a 3rd time but apparently don't think it's possible that Orpheus could be understandable of the party's and The Emperor's situation. Perhaps moreso The Emperor specifically as they want to be Illithid, seeing it as evolution.