I agree that the game was a work of love. I think Larian cares about and is passionate about Baldur's Gate, but that that care does not extend to the wider Forgotten Realms lore or the 5e ruleset. After all, the original BG games didn't use it, so I suspect their thinking there is that ruleset doesn't really matter. They may be right (they probably are right honestly) it's just a question of if the rules they came up with are actually better.
90% of BG3's rules match 5e's. The problem with 5e is that it's very hand-wavey and a lot is left up to DM fiat. A video game can't accommodate that, so they had to come up with other systems to fill in the gaps. I don't think straying from the RaW in the PHB indicates they don't like D&D's settings.
