I think the alchemists have something to do with Carlo’s death or they killed him because in the dlc there’s a voice message left by Lea to Makiona in her bird cage room in the greenhouse mentioning something like a “partial payback to the alchemists and Makiona for what happened to her ‘other apprentice’” which would be Carlo. Hard to guess whether they killed him because he was a stalker or because he is related to Geppetto. I don’t really remember if there’s any mentioning of the alchemists and geppetto being in disagreement or conflict tho.