If the Emperor is killed at the beginning of Act 3, the group is transformed immediately into Illithids. However, when the player decides to free Orpheus at the end of Act 3, the Emperor leaves, Orpheus is still chained, but the group is not transformed.

To fix this inconsistency I would suggest one of the following tweaks:

A) At the end of Act 3, let Orpheus or the narrator say something like: "Orpheus sensed the presence of the Orphic Hammer and protected the wielder of the only tool that could free him."

or

B) Let the metamorphosis happen when the player leaves the Prism, not immediately when the Emperor dies (or ad a narrator line saying something like "as you leave the Prism you are revealed without the Emperor's protection").

or

C) Let the narrator or Orpheus say: "Free Orpheus immediately (i.e. two turns or something) or lose your protection." An impossible task, without the Orphic Hammer.

I apologize if this has been suggested already, I didn't see it. And if there is another explanation for the different outcomes of removing the Emperor as your ally, please let me know.