I wonder if the dev team was uncomfortable writing a scenario in which making a “ends justify the means” decision ( which, to be clear, is genocidal) turns out any way other than unambiguously bad.
Specifically, so far as I can tell there’s little warning earlier in the game that the dragons are an important part of the magical ecosystem and have a role in protecting the Earth neither the player character nor Vauclair have any reason to suspect that killing the dragons might have world-ending consequences. Having watched playthroughs of the endings, including the consequences of the decision to side with Vauclair and kill the dragons, I came away with the impression that the game devs ended up adding a Deus Ex Machina to their “bad ending” to make sure everybody was clear that they’d made the objectively wrong decision.