Dunkelzahn isn’t even the only Great Dragon who dies - I distinctly recall Weisman saying that the events of the SNES game are canon too, which means Jake Armitage killed Drake. Sure, they added the caveat that Drake was supposedly young and underpowered, but you have that, you have the deaths of Dunkelzahn and Kaltenstein, you have Feuerschwinge’s defeat at a time before humanity was even equipped to handle the Sixth World. Would a dragon be so unstoppable in the age of Ares, Renraku and Aztechnology?
Setting all that aside, I’m still not seeing the basis for this comparison - Vauclair’s arguments aren’t gospel, and it’s completely self-serving for him to claim that all dragons are equally dangerous and that genocide is therefore the only option. You can’t extend that rationale to APEX because it’s a singular entity with a singular purpose. It offers no explanation for this supposed miracle of Monika’s ideals somehow overwriting its core programming; it demands you grant it control over a dragon and threatens you if you don’t; and if its actions ultimately protect the Flux State, does that justify the corpses it’s piled up to do so?