I think Larian should now write a "comic book" story relating the events leading up to the nautiloid attack.
I would suggest to work with the non-durge scenario. They should start with the separate backstories of Gortash (his childhood and rise as criminal in BG and how he became Bane's chosen) , Orin ( changeling origin and rise to Bhaal's chosen) and Ketheric's complex journey through sorrow, making him the Shar despot and later Myrkul chosen.
Then they can relate how the 3 dead gods planned to create the absolute and set the machine in motion, using their chosen to dominate the elder brain under moonrise towers.
They can then paint the backstories of the NPC characters ( including hunt for the artefact) and how they all get sucked into the nautiloid.
Some backstory of the artefact, the nethercrown and Raphaël would also be added.
Every time they hit a gap , contradiction or inconsistency they can make a decision to make it all fit together. Hopefully the emperor will disappear.
When the comic book is ready they can sell it, so the effort is not just a waste of time.
Then they can attune the game' s scenario so it matches aforementioned complete and consistent story.