Here's my take on all this with Early Access details fully taken into consideration;
All the evidence during Early Access supports this being the Emperor tadpoling the entire party after going rogue, because Daisy in EA would refer to the party as "her Chosen" and Shadowheart as "her beautiful weapon" as the prologue evidently displayed a clash between two different mindflayer factions aboard the Nautiloid (the Emperor making his move) because the mindflayer on the floor prior to getting tadpoled was already dead along with most of the Absolute cultists already mentally broken (which only a rogue mindflayer can do).
And considering how creepily manipulative Daisy was in EA depending on how the player treated her, the Emperor's personality behind the persona at the time was likely written to be 10 times worse because Larian clearly wanted him to truly embody what a mindflayer is. A heartlessly cold, calculating, manipulative psychic control-freak with far less moral ways to achieve his goal because he was quite literally willing to sacrifice the entirety of the Sword Coast using us as his Chosen, including us if we proved too stubborn. We were quite literally "his beautiful weapons", as Shadowheart still mentions even in full release.
Which is why Daisy was the way she was. She'd play nice as long as the party played nice, but if the party didn't play nice then she'd resort to direct threats and even force.
The essence of this personality still lingers even today in the Emperor although not as extreme nor direct, because if the player mistreats the Emperor in ACT 3 he will become very angry and show the party what he could've done to them by sharing memories of Duke Stelmane being dominated by him. Which fits his raw personality from Early Access because the tadpoles were a way for Daisy to initiate communication and slowly gain control over the player. The more the player used the tadpole, the stronger the psychic signal from it became which allowed Daisy to first only be able to communicate while the player was unconscious, and eventually even when they were fully awake. And if the player pissed her off, she would become furious and resort to direct threats (which we unfortunately never got to see, but we'd probably get dominated in certain parts of the story just like Stelmane was).
So I agree. This 100% was the Emperor in Early Access, however...
Because Larian noticed a vast majority of players kept entirely avoiding this aspect of the story since players couldn't for the life of them pick up on all the clues clearly hinting that Daisy ain't the tadpole nor the Absolute, this entire aspect of the game got rewritten and streamlined to make Daisy a benevolent Paladin Guardian instead who clearly stands against the Absolute, with the Emperor being much more emphatic and diplomatic in a friendly way as the focus of his narrative becomes the humanization of his character and whether his feelings are genuine or just an imitation.
He's doing what he must to survive because that's who he is, a survivor. A pragmatic whose most of his feelings towards our party are truly genuine because he could've done far worse to us, but naturally he's also simultaneously lying through omission by telling only what he considers important to tell to keep us focused on the job at hand. He has no use for petty human drama and trivialities, he's beyond such things because he sees the bigger picture when the fate of the whole existence is at stake, so who could blame him when he does truly end up saving the world and us multiple times.
Despite everything in Early Access clearly pointing towards the Emperor; in full release his appearance slightly changed to make him unique and the entire other half of the prologue that had all the evidence clearly pointing against him has been removed. Which is why the cinematic today is a sea of contradictions in relation to actual in-game lore due to the rewrites and unfortunately ends up being just a very fancy eye-candy intro cinematic and nothing more. One could say that he wiped our minds after tadpoling us, but alas the reality of the things is it is a very expensive cinematic created incredibly early during development so it no longer fits the actual in-game narrative because the party quite vividly remembers both the eye-insertion and the mindflayer who did it, yet does not whatsoever recognize the Emperor.
His Early Access version was a hardcore anti-hero who would have undertaken any action necessary no matter how immorally disgusting to achieve his goal and would have dominated us without any hesitation once we pissed him off. Which is an era of the game when the tadpoles and choices around Daisy truly were a severe consequence both in terms of gameplay and roleplay.
