I don't consider it to be one unified story at all, I mean some of the series obviously are connected, but the rest are, as the name suggests, legends about Zelda. Unconnected unreliable narrations about some sort of heroic past events. Everybody agrees about the characters involved but as to what exactly happened, that is lost to time. So each culture is now telling the story a different way, emphasizing whatever is important to them.
I consider as a sort of modern equivalent to the coyote stories. or Paul Bunyan, Finn McCool, Gilgamesh, Or really, any legendary heroic epic passed along by oral storytelling.
So it is fun to try to fit it into some sort of unified timeline. But I don't think it is, that is not how they were actually written and we would loose most of the interesting storytelling flexibility if that is how they write them in the future.
Many of the games include histories within the current telling, histories which include past versions of Gannon, Link, and/or Zelda.
It's pretty clear that the cyclic nature is a part of the story.
I prefer this interpretation, but there is just so much textual content in the games which support a unified branching timeline for most of the games. You can start with the explicit chronologies you have and mostly put them together like a puzzle. Zelda games which don't explicitly position themselves in chronological relationship to another Zelda game are the exception (like OoS/OoA or the Four Swords timelines).
This is not a deep-Zelda-nerd take, this is mostly working with simple connections like "Zelda 2 is a sequel to Zelda 1".
I think most Nintendo IPs are about playing around with the same motifs, ideas, narratives, and gameplay elements. Metroid is another series where this is very evident, with half of the games being spiritually a remake of a game which game before. A timeline doesn't preclude the Zelda series as a story about the cyclical nature of conflict, about archetypes reappearing throughout history, or as a legend passed over generations.
That's similar the way I think about James Bond. He's not one singular person, but a code name given to an agent in deep cover. The agent, the person changes through the decades, but the name lives on.
While I agree in spirit and think that was true for most of the games when written, there has been an official timeline published by Nintendo[1,2] since 2011 (and the idea was apparently around internally since 2002).
I would be surprised if it did not have some impact on the writing of the games, though of course there is (as of yet) no explicit reference to the timeline in the games.
[1]: https://zelda.fandom.com/wiki/The_Legend_of_Zelda_timeline [2]: https://zelda.nintendo.com/about/