There was always an Emperor it's just that it was a different character.
I remember there was a datamined line about how terrifying a mindflayer emperor is. There is also the MtG card showing what looks like the Emperor (blue eyes though) tadpoling someone, "Your mind belongs to the Emperor now".
Looking at the appearance of the Emperor he is larger than the other mindflayers and is dressed in a more regal manner. I think originally, the guardian(Desire) was Orpheus and the Emperor(Daisy) was meant to be the restorer of the Illithid Empire. This would explain why if you side with Orpheus he says he's putting an end to the nascent illithid empire and why the Emperor randomly decides to join the brain. So, yeah I think the original Emperor tadpoled us.
This changes when Larian decided to turn the Emperor into the guardian. It's pretty obvious that the Emperor backstory cutscenes were added pretty late since they're not even animated. Him being called the Emperor because he controlled trade or something is such a poor cop out. Which means whoever tadpoled us is some random irrelevant illithid which makes the cinematic also irrelevant.
I guess all of this fallsunder the guise of "subverting expectations" AKA terrible modern writing?
