Empy doesn't take over until we take out these gith monk guards.
I’m suggesting the pre-Emperor inconsistency is related to Orpheus being an actual sentient being who controls that power, even if he is imprisoned for it. Early on, Shadowheart says the Prism has a will of its own, meaning it has to be his will or at least an extension of it. Anyone who is ever alive is inconsistent sometimes so that’s just what I concluded in my head.
EDIT: It would be inaccurate to say The Emperor doesn’t take control until after the gith guards are taken down. I remember he was shown to have control of Orpheus at the start of the scene, but it broke the moment one of the gith guards punched the barrier. So yeah, I think that inconsistency can also be attributed to the fighting that has been going on all this time. Feel free to criticize them for not showing that clear enough though.