Las propias palabras de Miyamoto:
Many have wanted the Zelda timeline to be fully explained when it was our wish to never have a solid chronological order so each Zelda game could be more unique. For the original Hyrule Historia, we struggled to connect games that seemingly have no proper ordering when Eiji Aonuma decided to add another timeline to the series to make it easier for us. Since the introduction of Skyward Sword, Aonuma found that adding more timelines would please both fans and ourselves for the fans who want a fully explained history and ourselves who want a mysterious history. This new fourth timeline will be used for future titles or maybe it will not. Time will tell.
Basicamente, muchos fans querian la cronologia bien explicada y que tras Skyward sword y la tercera cronologia que daba sentido a los juegos, Aonuma decide añadir esta cuarta cronologia que podria ser usada en futuros juegos. O no