If we can't ask he Emperor directly and be told directly that he doesn't know, then we as players are just being presented with a very knowledgeable individual who reasonably would have insights and not being allowed by the game to ask for those insights.
These tadpoles are tainted by the Nether, no one can be sure of anything at this point but the most direct answer could be this line:
"The Emperor: I've been studying you for a while now. I believe I can trigger the next stage of your tadpole's life cycle while continuing to preserve your independence."
("Meticulous Notes" evokes a kind of assimilation but not sure if it could refer only to Tav/Emperor or Nethertadpole/host too:"[…] how does the presence of another's mind within one's own affect the body? […] If such an experience leaves behind a permanent memory, is that part of your mind still truly your own?")
There's a lot of interesting ideas to exploit and I would like to play the OP alternative version if a campaign editor came out, but I'm not fan of the trust/distrust feature.
The Emperor looks like a guy with 200 IQ who finds no interest in discussing with the children we are or spending time explaining/justifying his behaviour to inferior beings. He does only when he is forced and then, yield only partial information.
Everything he does or says serves a purpose, strong motivations would be required to force him to become more present during the adventure because as it now appears, he only reacts to things that may threat his goal and for optimizing chances of success by coddling the avatar to embrace at least partial-ceremorphosis, nothing else matters.
Just another opinion to add to the pile though. Despite multiple run (and even datamining), we all continue to interpret him in a very different way.
