I'm pretty sure that is answered by digging into the brains of True Souls and even Flind the Gnoll Warlord, where we see visions of them all being taken to Moonrise Towers and infected with a tadpole, which then binds the individual to the Absolute through a special magical ritual and them being unaware of the tadpole. So the tadpole on its own doesn't prevent enthrallment and ceremorphosis, it needs to undergo a special magical ritual once the host is infected in order to become a True Soul. Also if you look at True Souls, none of them experience pain or discomfort from its psyonic advantages.

The Dreamer (artifact) however managed to stop this on its own without the ritual by placing it in stasis, but at the expense of us being aware of it and it hurting us if we overuse it because it is not dormant. The tadpole is also actively fighting against the Dreamer and trying to kill her, because the Dreamer is preventing it from fulfilling its purpose. Remember that it tried to ceremorphosize and made us very sick, but the Dreamer stopped it. Which is why the Dreamer is also very insulted if you act ungrateful and accuse her of trying to kill you.

As for the civil war theory, the reason why I believe it's a civil war between Absolute mindflayers and regular mindflayers is because the cinematic shows some of them already dead and the Mindflayer who infected us looking at their corpse in a dismissive sort of way, before the Githyanki even arrive. Also the enthralled people on the Nautiloid are wearing the Absolute necklace, yet they lost their minds, which leads me to believe the Absolute party invaded the Nautiloid and the psyonic skirmish between the two caused them to go insane. Because the mindflayer itself serves the Absolute (found out later during Ragzlin's interrogation) and they don't attack their own followers. So the only ones who could have done it were other mindflayers.

As for Astarion and Wyll, Astarion himself says that he was saved from Cazador by being snatched away from him. Since Cazador lives in Baldur's Gate and Astarion is a slave kept in a cellar feeding on rats, it gives me no reason to believe he was taken from anywhere else. Same for Wyll who is the legend of the Gate. The only one I don't know where he was taken from is Gale. He can be with us initially already or taken from Baldur's Gate too.