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evidenced by the fact that everyone and their cat tells you that ceremorphosis happens very quickly after infection and that you are walking around normally is highly irregular

A regular 2e-ceremorph infection would have no "True Soul" stage. It's more like an infection with Naegleria fowleri with the tadpole eating most of the brain except for the parts it still needs to regulate bodily functions and metamorphose into a mind flayer. The (usually abducted) victims waste away within hours or days, and the mind flayer that later emerges would then need another twenty years raised by their hive to reach adulthood. Therefore, the Absolute plot did indeed produce very special tadpoles.

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Also note that when you win the last battle, you command the netherbrain to destroy all tadpoles first and then itself. That also indicates that the worms will outlive the Netherbrain and turn their victims when it is gone.
I didn't remember this bit, but you're right. The question is, does this only affect any tadpoles on the loose or also those which have already merged with a host organism.