Exceptions do exist, but they are mostly regarded as the worst examples of these tropes. The best examples turn great narratives in the best stories ever told. Note that, despite the name, the villainous parties of the narrative don't necessarily have to be formally connected, they can even act against each other if motivated to do so.

Heir To The Empire, as a story on conflict, has figures that potentially fit the bill, but are beyond the pale of the current story framing.