I expect that a Warp in the North is unlikely. They probably won't want to default to that solution every time they come up with a quest that gives the player multiple outcomes. That's unwieldy.
I do think it's more likely that it will be "unclear" who won the war, but that the Empire collapses, receedes, or withdraws in the longer run. In other words, even if the Empire beat Ulfric with the Dovahkiin, the Stormcloak movement ultimately succeeds.
History books in this game don't really talk too much about the "Faction" accomplishments of the Nerevarine, nor of the CoC. The books, for the most part, only recognize main quest events. In other words, you don't see history books in Skyrim about the COC being the head of the thieves guild, that person is just a mysterious actor in collusion with the Grey Fox. Likewise, there aren't any books about what the Nerevarine did for the Mages Guild in Morrowind.
Nope, those accomplishments are usually left out, and attributed to some random prominent "person." Likewise, I don't think the Dovahkiin will get credit for taking sides in the Civil War, regardless of the fact that the player can actually do that in the game.
It's more of a faction quest than a main one. Sadly, I think this is the most likely outcome.