Who in your theorizing is Withers referring to when he is first disinterred, when he says something to the affect "It is as he fortold" before going into his 'what is the value of a mortal life' spiel. Clearly the events of this adventure were foretold, but to what end.
And as you've said, mind-flayers don't have souls, and there's another line in the game that says the worship of the mind-controlled doesn't empower deities, this is part of my confusion around the Dead Three's plot, apart from Bane for whom dominating the world seems pretty on brand. I'm also wondering if by relinquishing his, or some part of his, godhood Jergal is considered to be grandfathered around the limitations put on the other gods.

As I've been playing through my second run, I've been trying to pay more attention to the timeline of events.
We know that the main plot was devised by Gortash, Gortash was sold to a devil, Raphael specifically, when he was a child, freed himself I forget how, rose through the ranks of the criminal underworld encountering both The Emperor and Karlach. While the heist to steal the crown probably took place ~10 years ago, he can maybe assume he became aware of it while sold to Raphael, when during all of this Gortash fell in with Bane is also unclear to me, but The Emperor refers to him as a Banite when he knew him.

Another point about the colony beneath Moonrise. We learn that it went dormant from lack of resources, an unclear but likely extended period of time ago, there's a slate you find in the colony which reprises the reawakening of the colony, by three stones of power which then enslaved the hivemind. (unrelated we also learn that the original chosen of Bhaal is Orrin's brother) This might explain why there's a lot of otherwise rare Illithid tech involved, but more difficult to square, this means that underneath Moonrise Towers, a Selunite stronghold, is a dormant Illithid colony, the ancient remains of a Sharran settlement, upon which Ketheric Thorm built a second Sharran settlement.

All of this is supposed to work itself back into a grand scheme by Withers. Possibly dating back to the Netherese?