In fact the thing about mindflayer souls seems like a really philosophically interesting, thematically rich topic the likes of which all the best CRPGs grapple with, and I'm particularly sad that it's glossed over.
I believe it goes against the lore. While BG3 is my first game from the BG series, I am pretty sure it was clearly stated that you must have a soul to cast magic. And there ARE wizards among mindflayers.
Crown
We don't get to decide what to do with the crown? It just falls in the river and that's it, aside from a few lines for Gale? It seemed like it was set up to be a much bigger deal than that. I was sure we'd get to choose to give it to Mystra or Raphael or destroy it, or claim it for ourselves, maybe in some kind of elaborate secret ending where we ascend to godhood like in a certain other CRPG.
You have to play as Gale as your Main Character to get proper ending on this.
It's a bit more complicated, because Illithids do have a deity, so they must have souls, just probably a significantly different manifestation of it compared to the domains of the other gods, which is probably why Jergal won't acknowledge them.
Another problem with these endings is that they make post-game DLC very difficult to pull off, because how can you possibly continue a campaign in which your character has been supplanted by an illithid? It would require such drastic branching, and gives little opportunity for customization because they'd have to fit all the new armors and weapons onto an illithid body, and the epilogue as it currently exists anyways tells you that you feel your mind slowly slipping and becoming more calculating and manipulative with a hunger for brains.
They really put themselves in a Mass Effect 3 pickle with these endings that force someone in the party to become an illithid.