That's true, of course, since it's fiction. A change in the way the story depicts its universe doesn't mean the universe has changed, just that the way it's presented to us has been refined, so that the earlier version can be presumed to have been an inaccurate account.
But it's worth noting that SNW: "Tomorrow and Tomorrow and Tomorrow" made it canonical that Temporal Cold War factions have rewritten 20th- and 21st-century history from the way it was in TOS, where the Eugenics Wars happened in the 1990s, to a timeline more like the present, where Khan is still a child in the early 2020s. Yet the assumption is that eventually the timelines more or less converge again so that the 23rd century and beyond remain pretty much the same. Still, it opens the door for more departures from continuity if future writers wish it. Trek has never needed a time-travel excuse for its continuity changes, you're right about that. But it does now have one.