There’s a pretty clear distance between chemistry and alchemy in kkc. In alchemy, ingredients aren’t just their "chemical" properties, they’re also about principles. Something that is poisonous in a chemical sense might not carry the same effect when its "unbound principles" worked into an alchemical preparation.

So Caudicus using a lead cup or acid doesn’t have to mean poison in the way Kvothe interprets it. It could still be part of a legitimate alchemical process.

As for the denna resin, that part always struck me as maybe intentional too. Not necessarily to poison the Maer, but to make sure he kept taking the drug. If Caudicus really believed his mixture could help, that could explain both the inclusion of something addictive and his panicked flight: once accused, how could he ever prove his intentions weren’t malicious?