I don't think we have much reason to consider San's having resistance negation since we know that magical attacks that monsters use exist physically as well. The bones that Papyrus has saved up from battle and undyne splitting the bridge with her spear. Plus, monster bodies are made of magic so their magic being able to interact with each other even if lacking a soul makes sense. Not to mention, you can still lost fights with monsters and die as Souless Frisk. All of these things combined, I don't think gives enough support that we'd give Sans reistance negation, they're just attacking on two levels. Plus, we see the likes of Toriel able to harm flowey so Sans wouldn't be unique and all monsters would qualify for reistance negation in this case. And the most important thing here, is that you can't negate resistance when they character lacks a key attribute that would require resisting in the first place. Flowey has no soul, so no soul manipulation should work on him. Therefore, he's just dying to physical damage as seen when he's killed in Genocide Runs