I played through the game and its expansions (but not Deadfire) and very much enjoyed them. The classes, spells, resolution mechanics, and itemization were all things that made sense to me. But I never really grokked the ability scores; to me they feel inconsequential except at the extremes. Lots of build guides have weird design artifacts like max Intelligence, low Constitution Barbarians (because their melee attacks are AoE and Intelligence makes the AoE bigger, and they can use polearms to keep out of reach of being attacked).I couldn't get too far in the game, I have other issues with it. But I wholly agree with the challenges he took on as a designer, whether he succeeded or not.
I agree with you that some of those design goals are good ones, but I think the mechanics they arrived at break down if the fiction behind them needs to make sense. That works in a CRPG but is otherwise a pretty major problem.
There is probably a more conservative solution (elegant as you put it) that would result in better build diversity.