Karlach's dock scene does not depend on the player character, it depends on Wyll, the player character isn't even necessary for it. Wyll makes the offer to accompany Karlach and if you tell her to do what she wants, she goes with Wyll. However, if the player character is not present anymore, because they killed themselves, rode off to fight in the rebellion, have to hide behind a box - or before patch 5 talk to Mystra - Wyll does not make his offer and Karlach explodes. Allowing for Karlach and Wyll to have their Avernus ending would simply require them to make the same choices they autonomously make when the player acts as a silent observer to the scene. It would then, as Fylimar mentioned, be another of the endings in which the lovers (or friends) meet again after six months apart, of which there already are several.
I don't want to get into your dubious interpretation of improving Astarion or Karlach's condition - because you can of course "fix Karlach's engine" by turning her into a mind flayer.
Exactly. And I think, Astarions ending as spawn was mentioned as being polished and fixed in the patch notes.
"We are all stories in the end. Just make it a good one."