Difficult != impossible. I would assume many ideas were worked through as consequences to tadpoles, ultimately none of them ended up in the game. Maybe they forgot?
While BG3 is a huge breath a fresh air and shows an intrinsic desire to make a great game vs a great product, Larian is still in the business of selling games. This game in particular, isn't even their own IP. Obsidian spent over a year trying to broker a deal for BG and wasn't able to get a licensing agreement. I highly doubt WotC/Hasbro just said "Hey just kick us 20% and do whatever you want."
I agree with a lot of the sentiments regarding the overall plot, being railroaded at the end game, do whatever you want as long as you eventually pick the right choice etc. I would guess a lot of the narrative issues stemmed from not owning the IP. The infinite iterations of sending it up and down the chain to WotC/Hasbro - many of whom are very much on the side of having a great product. At some point there's no more money, there's no more dev time, you have to release. Maybe Larian had full creative control and all their writers just suck, maybe Mearls has a serious Mindflayer fetish. I can only speculate, and I do think having insight into the more business side of development would be really interesting.
I actually seriously doubt WoTC had anything to do with it. Having their narrative (and their gameplay) fall apart in the last act is something Larian had a history of in their games well before this.
