As far as I'm concerned mind flayers are just zombie wizards. They need to eat brains and can only reproduce by infecting others. And the process destroys the host. Sounds like Larian was trying to add Mass Effect indoctrination into BG3.
I'm pretty sure both Emp and EB are following the mind flayer grand design but each one wants to be in charge. And Emp would rather be a pawn under EB's grand design than deal with you as an equal. I'm confused about the dead mind flayer bodies in the nautilus intro scene, though. There was no sign of battle until the Githyanki showed up so Emp must have killed his friends (but left the pilot alive... so maybe he was the only other mind flayer in on the plan), infected you, and jumped into the rubiks cube (which was located in Shadowheart's locked pod). I'm surprised you can just free Orpheus like it's no big deal considering you have to pass will checks every time you try to go against the parasite.
