NPCs with plot armor, does it bother you?

[Kallera]

This logic fails because villains that appear in side stories can be encountered after they have been killed in the MSQ. The biggest and most obvious example of this is Nidhogg and his eyes, which was present in the ARR DRG job quests.

That is not plot armor to begin with. plot armor is more along the lines of "eyeless Nidhogg surviving long enough to get his eye transplant by Hreasvelgr." And there are more examples on the heroes side than the villains.