You know from Astarion's origin run that he's actually right there on the boat next to the docks, hiding on the ship deck. They wouldn't even have to change the order of the scenes. There could just be a scene where the player goes over to make sure he's okay before Karlach's scene plays.

They changed the companion lines to be nicer but that was never really my issue with it bc I'm not supposed to be able to control their personalities. It's just really jarring to see a companion your MC might care about run away on fire and not have the option to uh, make sure they're alive and okay lol. In my first playthrough I wasn't even sure if he died and it took me out of the rest of the ending. This was when the game first came out so Karlach's ending was still broken and didn't play, which I'm glad about because I would have been distracted the whole time if it had. As it was it just skipped right from Astarion running away to all the NPCs in the city who I had no emotional investment in celebrating.

They've added so many scenes for the companions since release and this to me always felt like the result of them deciding to cut the game off at the docks right before release, so I'm surprised they didn't change it. I don't know if they're allowed to add new dialogue and voiced lines going forward beyond what they already had planned when they ended their deal with wotc, but it would be nice to at least have a cinematic for it.