Wind Waker is the Child Timeline, isn't it? The alternate future where Link went to Termina, and so Gannon went unopposed and flooded the world.
Wind Waker is adult timeline so it's a world without the OoT Link cos he left to the child timeline which left the world Linkless which meant the flood had to happen.
Also with the timeline, Hyrule Historia lists the official timelines so we can know what game is in which. Though the official one worked out the same as the one the fans came up with because Zelda fans were smart and figured it out