Good points and a good question. For this matter I would consider BG3 its own rule system with many spells that could solve this or that problem simply not available. If I was a DM in a post-BG3 scenario, I'd probably rule like this:

With the Absolute gone, any powers it kept up (think concentrations) dropped, which may explain why Astarion was no longer protected from sunlight and Karlach's heart finally failed. Can the tadpoles be removed? During the game, there are several instances where someone is sure they can remove the tadpole, only to find that these are different. The question here is, if this was due to the Absolute's active protection, or the nature of the tadpole and its link to the host. Let's assume we want to keep them, or removing them would be too dangerous. Ceremorphs don't necessarily die when the elder brain that spawned them dies. When illithid tadpoles don't find a host in time, usually because something destroyed their colony and no one brought them any, they can grow to enormous proportions. So, they could also theoretically live on in the people who were still in suspended ceremorphosis when the Netherbrain died and just keep doing their thing.


Unlike regular tadpoles, the Absolute's modified ceremorphs left much of their hosts' brains and personalities intact while in suspended ceremorphosis. The Astral Prism protected the Emperor's chosen from being turned by the Absolute, which could be read as a clue that this is something the Absolute had to do consciously, i.e. keeping True Souls humanoid, while choosing to turn others earlier. Without that trigger, an infected host would stay in suspended ceremorphosis. That would leave our group with their tadpoles in something like symbiosis and future adventure hooks galore. Even if you carefully picked up all the conspirators' paperwork and exothermically cleansed all the labs, a host of villains will probably stand at the ready to hunt you for experiments to gain these powers themselves or raise their own army of half-flayers. The mid-term question would be, how stable such a symbiosis would be. Would you eventually grow tentacles, or get sick when your body eventually rejects the tadpoles?