While this issue exists and it's definitely the case( like if I play with a friend we have 2 parties of 2, that's just how the game is coded) I would say it feels significantly better than during the EA. Mostly due to couple interactions I've seen.
For instance dark urge+shadowheart and gale+ karlach party will make shadowheart questline available only to dark urge and I can only watch karlach questline unfold.
But while talking with shadowheart she will still share her thoughs about karlach's questline so it kinda " glues " both parties together in-game.
if you add to this the very ocasional and rare but still, party banter + some comments they make mid-dialogue with others and so far I think it's quite ok. Could be better by virtue of " more" interactions of this type but still I feel like Larian at least tried to address it.
So far most of my fears from EA were addressed and I'm having a blast playing this game. It's just so great so far I'm lacking words to describe it. But yes, the coop integration does make a couple scenes here and there very weird / out of context. Especially the below.THe spoiler below is a real huge spoiler. Do not open it if you didn't finish the shadowheart quest line.
Within the shadowheart questline at some point in Act 2 you go through Shaar trials.
If your friend is a troll, when you're about to enter the final area he teleports in front of you , and enters the final area first.
From now on, the couple cinematics in there considered his character as the protagonist of the story despite acknowleding Shadowheart is the disciple of Shaar.
It worked in the end but the game clearly had issues understanding what is actually hapenning and who is who.
I'm in Act 3 and my character is still talking about " Nightsong will speak to shadowheart when she's ready". Like...it already hapenned. In Act 2.
They've talked it through, the questline moved forward.
But whatever hapenned in Act 2 ...yes. The game struggled.
Since any player can be any character at any given time the amount of permutations is so insane I'm still impressed Baldur's Gate 3 doesn't crash on launch. But yes, it's not perfect in creating a " unified" party in coop.