> Shigeru Miyamoto: For every Zelda game we tell a new story, but we actually have an enormous document that explains how the game relates to the others, and bind them together. But to be honest, they are not that important to us. We care more about developing the game system… give the player new challenges for every chapter that is born.
So I don't think this is as clear cut as "a different group of people decades later make a timeline". The least charitable view might be that they never intended the unified timeline thing to became public and didn't consider it "lore", but I'm not sure I buy that either (since they talked about some details in other interviews, including the Victorious/Fallen Hero split most people object to).
[1]: https://www.nintendoforums.com/articles/40/super-play-magazi...
Nintendo just never did that until the speculation about the topic became noticeable enough that they felt they had to address it (at which point everything was so inconsistent that only the timeline split could reconcile it). And even then, the unified timeline was published years before BoTW, and it adds the wrinkle that... (waves hands) all of the timelines sort of became the same thing.
That sort of hand waving is unavoidable as BoTW has elements from all three of the timelines, it literally cannot be on one of the three legs-- and if it's not, the only other logical place it would fit is before Skyward Sword (meaning an entirely separate ancient founding of Hyrule) or just after the Imprisoning War which would butt up against A Link To The Past. But those can't fit because the Zora evolved into the Rito and BoTW has both.
Never mind the strange notion that a fish people evolved into bird people under the pressure of a worldwide flood... you'd think that wouldn't be necessary or helpful, but hey, Zelda's weird.
Mostly in jest, but isn't that a creationist argument we all usually dismiss? "Why are there still primates around if we evolved from them?"