It's clear Jon doesn't mean Starks and Targaryens. You think a little snippet about a short period in such a long history would be on D&D's radar to the point of having Jon make note of it? Something that's not even mentioned in the main story? 'Fighting together against a common enemy for centuries' wouldn't even fit in with that excerpt. And I'd think he would mean WWs as the enemy. They'd been gone long before Targaryens even existed. Those two families had little in common in the past.