The interviewer asking if the Emperor was always a squid was so stupid. We know he was always a mindflayer from the MtG card. However, the MtG card shows him tadpoling someone, "Your mind belongs to the Emperor now". The interviewer should've asked if he was the guy who originally tadpoled you.
Wasn't there also a datamined dialogue about how terrifying a mindflayer emperor is (where do I find all the leaks again)?
I believe that his name originally signified that he's supposed to be the restorer of the mindflayer empire. His backstory cutscenes about his adventuring days and why he was called the Emperor aren't even properly animated that they were most likely a very late addition to explain his peculiar name. Seems to me that originally there was a three way mind battle between the tadpole (Emperor), prism guardian (Orpheus) and whatever the original dark urge was.
The act stuff also goes back to celestielf's comment on the structure of the game. I'm not sure if it's just me but I kind of feel that I have no direction without a proper villain to chase, especially considering how great some CRPG villains were. Taking a look at DA:O where you have to get to Loghain before you get to the Archdemon. In this case, Ketheric, the only good villain in this game, is Loghain and the Netherbrain is the Archdemon. But wait, once you kill Ketheric you gotta fight more super duper bad guys for almost every origin. Yet if everyone is super duper special then no one really is. Add in the fact there is probably a lot of cut content involving these villains. God damn, the origin system is so bad.