It's a fair point, but Nintendo is the only entity that can decide canonicity, and retconning continuity is far from uncommon especially when a franchise transitions from being a single entry to multiple installments.

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.