Events of the Orpheus ending create a situation where the Emperor had to be lying, there is no other excuse for his JOINING the brain, which would otherwise be out of character for him. Larian chose to write that as an alternate timeline or something, but his behavior in that ending lays bare that he had to be lying the whole time (which is something that doesn't happen in the endings where you do not betray him).. In effect the story's universe changes at that juncture, and the facts of the matter fundamentally are not the same as the endings that occur if you stick with the Emperor.
That could be right. Or it could be that it's a situation like Nyrissa the displacer beast. Nyrissa can die (or join Yuigur in hell) thinking she is the heartjewel of the devil. But if you do some investigating and a bit of spider licking you can find out that Yuigur is holding her in thrall. This seems like foreshadowing for the freeing Orpheus moment.
*Puts on tin foil hat*
I'm not sure we can trust the narrator when we are talking to The Emperor. The narrator tells us that Orpheus will try to kill us but later both Raphael and Voss tell us he won't and they turn out to be correct. When we are standing in front of the Emperor the narrator makes the best possible case for consuming the astral tadpole as a a process of evolution. But it's not, it's a withering of the soul, a loss of the self or - as @anska has suggested - feeding an addiction.
We are like Nyrisa - the mindflayer used charm person which leave us vulnerable to its manipulations. Orpheus was always a threat to The Emperor but never to us.
Raphael: Charmed, I'm sure.
In more ways than one . . .
