The Elder Scrolls universe has an in-universe explanation for contradictory lore outcomes. It is called a Dragon Break.
When multiple players make mutually exclusive choices that all count as canonical history, Bethesda’s solution is not to pick one outcome. Instead: time fractures, all outcomes occur simultaneously, and reality reconciles later. This is documented as an actual phenomenon within the lore. The most famous example is the Warp in the West from Daggerfall — six contradictory endings all happened overnight, permanently reshaping the political map of two provinces. Nobody in-universe fully understands what occurred.
Skyrim’s civil war has the same problem.
Side with the Stormcloaks and Ulfric takes Windhelm, independence is won. Side with the Empire and the Legion holds Skyrim. Never touch the questline at all and nothing is resolved. All three are valid playthroughs. None of them can be simultaneously true. The next Elder Scrolls game still has to deal with the state of Skyrim.
A Dragon Break specifically requires conditions significant enough to split outcomes rather than collapsing into one. The Dovahkiin qualifies. The main questline involves a time wound at the Throat of the World and an Elder Scroll being central to a pivotal battle — the exact elements involved in previous Dragon Breaks.
The Thalmor add one more factor. They are not trying to win the civil war. They are trying to prevent either side from winning, because a prolonged conflict weakens both the Empire and Skyrim. Deliberately keeping a wound unresolved indefinitely is exactly the kind of temporal interference this universe treats as dangerous.
Whether Bethesda commits to this reading or quietly declares one ending canonical remains to be seen. They have done both before. The Dragon Break interpretation fits the available evidence. The alternative — simply picking a winner — would be the less interesting choice.