Would take a lot to convince me that a story NOT including the Dead Three would be more compelling to BG/DND fans. I love the idea of Atropus though!
Knowing Larian's favouring of ships in recent games to facilitate travel to new locations, it wouldn't surprise me if 'joining' the gith legion (or at least temporarily being allowed to fight beside them) would be an option in BG3 via spelljammers/nautiloids
Is this something the Illithid would even allow? Their disdain for life is immutable right? Perhaps if an Elder Brain commanded so?
More research required my end I think.
Oh I have no doubt that the Dead Three are going to be in the plot of BG3, but in an interesting twist they might be potential allies, even evil Gods hate and fear Atropus, and it is dangerous enough that good and evil and chaos and law might set A-side their usual feuding to face that sort of threat.