I am a big fan of the Baldur's Gate games and the Divinity games. I also regularly play tabletop 5e.
It seem to me like Larian doesn't really understand the appeal of tabletop 5e and isn't giving it a chance.
It feels like they are trying to adapt Divinity rules with a 5e paint job rather than starting with 5e rules and working from there. It was mentioned early on that they didn't think people like to miss so they added a bunch of extra rules to improve hit rates or give advantage.
The problem with meddling with 5e rules that it unbalances things. Elevation bonuses benefit ranged characters, but punishes melee. Then more rules need to be added to counter the other rules and more and more. Jumping/Disengage as a bonus action spits on the rogue and monk who lose a class feature.
It isn't necessary. Playing on a tabletop it doesn't feel like you are always missing, there's bounded accuracy and monsters designed to be either low AC/high Hp or higher AC/low hp.
I also think that if instead of showing a percentage attack change and people goiing "HoW cOuLd i MiSs aT 99%?!" just show the roll. It gives more feedback than just hit/miss. Missing three times in a row could be rolls of 1, 2. 3 or 8, 9, 10. It just feels better when you miss by less.
I think that Larian has made everything much harder for themselves trying to balance things and could potentially alienate fans of the 5e ruleset by having things that would never appear in tabletop play.
An example that bugged me was an open wound disease that over a few turns progressed into a disease that gave vulnerability to all damage that required a second level spell to remove at level 3 play. Diseases are relatively rare in 5e, and usually progress over days, not seconds. it shouldn't be a thing that every trap does.
Anyway, that's just my thoughts.
I think you're very much right that this feels like an attempt to adapt D&D ruleset to the game engine, rather than adapt the game engine to the D&D ruleset. A minor, but crucial distinction and in my opinion the wrong way to do it.
I suspect that Larian has made a bit of a mistake in modifying the D&D ruleset before beginning Early Access, since now all of us that actually knows the D&D ruleset might feel that it would have been better to implement the rules as directly as possible instead of some of these odd adjustments. Combined with a lack of a available roadmap/design document it's really hard to tell which D&D features have been removed or modified, and which just haven't been implemented yet. And then the paranoia starts....
Edit: I won't comment of the parts of OP that misunderstands either of the systems as they seem to have already been corrected by others
