I agree that there are a few plot holes regarding the tadpoles.
- There is an established narrative that tadpoles leave the body upon death, but there is no explanation why this doesn't happen to the PCs
- There is no reason given for why you cannot just crush someone's skull, kill the tadpole, and resurrect the character
- The explanations for why ceromorphosis is not occurring and the development of a "symbiotic" relationship (i.e., tadpole powers) are weak and non-existent respectively.

This feels like lazy / unimaginative writing to me. Or perhaps someone just decided that giving everyone tadpole powers would be "cool" without thinking about how it would affect the story.

If it up to me, the tadpoles would leave the body upon death and crawl back in upon resurrection. There could be some high (perhaps impossibly high) skill check involved if you want to try and prevent the tadpole from crawling back in. I would also recommend Larian either ditch the tadpole powers completely or provide some plausible explanation for the development of these powers and a drawback (like loosing control of your body to the tadpole).

My preference would be to just remove the tadpole powers completely and just have the tadpoles be dormant, at least until you arrive at Moonrise Towers.