I wonder how strong "canon" can be when it appears nowhere in the actual games themselves. The "official" timeline has been revised on more than one occasion. If a new idea for a game contradicts the timeline few are going to care.

If a story doesn't appear in the media itself, it's really just commentary, and far more mutable than anything in the actual story.

Contradict the events in Wind Waker and you are messing with people's memories and ability to suspend disbelief. Put "Wind Waker" in a new timeline and few are going to even notice.