I wonder if they can't fix it, because they didn't record any dialogues for these paths (Illithid Alliance and Stayed together with Illithid as friends flags).

I mean, Astarion still has no reaction to being kidnapped and saved, just like Tav and companions. Not even in the datamined files.
So it's totally possible these dialogues just don't exist here as well.

Still, I think, AA staying together with M!Tav is extremely jarring, even without existing dialogues, this should be fixed to them being separated and preferebaly the flag which states they were together needs to go, because after all the vile AA's comments about Illithid Tav it looks very weird when he calls them "my love".