Within the Zelda canon, there is the timeline, but there has always been the sense of the main story and kind of a side story. Like, Majora's Mask might be considered part of that, though it does exist as part of the timeline. With Hyrule Warriors, there is a link between the two, but it exists as a separate dimension, so it doesn't exist as part of the main canon. Lately I have been thinking of it similar to The Avengers. - Eiji Aonuma