It's like with Zelda. The timeline only matters if the writers for the current game think it does. What matters is right now. Later devs/writers are free to ignore to ignore or alter the timeline as they please.

Somehow, I can't imagine that when they're making a Zelda game and someone comes up with a cool idea, someone's gonna show up and go "No, that contradicts the timeline". If the idea's good or useful enough, they'll let it be used regardless of how it fits.