The answers to the "Timeline" is simple.
They are legends. That's it.
Legends turning out to be true is an incredibly common trend in the Zelda games,
Zelda 2: Link is told about an ancient Princess Zelda who was placed under a sleeping curse by a wicked magician. He is then shown this sleeping Princess Zelda in person, revealing her story to be more than mere legend.
ALTTP: The Imprisoning War and all that led up to it happened so long ago that they were considered mere myth by the present day. As Link rescues each Maiden, he learns more and more that the Imprisoning War and its prewar events were actual history.
OOT: The Triforce is considered a legendary sacred object left behind by the goddesses who created Hyrule and is said to grant any wish of the one who touches it, or else it will split if the one who touches it has an unbalanced heart. All of this proven to be true when Ganondorf enters the Sacred Realm and touches the Triforce, as recounted to Link by Rauru and Sheik.
MM: Link is told by Anju's grandmother of a legend of the Four Giants who once lived with the people in the land of Termina before having to leave the people and go guard the four corners of the world, leaving behind an "imp" who was once their friend and who lashed out in anger and sadness over their departure before the Giants returned to tell him to knock it off and Termina or else they would have to kill him. Link is also told about the Skull Kid's past by Tatl and later witnesses a reconciliation between the Skull Kid and the Giants, revealing that the imp in the legend was actually him, and that the events in said legend actually happened.
FS: The manual tells a tale of the wind sorcerer Vaati who once terrorized Hyrule and kidnapped girls before a young boy armed with the Four Sword went on to defeat Vaati, seal him away, and rescue the girls. The game then opens with Vaati escaping his seal within the enshrined Four Sword and kidnapping Princess Zelda, revealing the story in the manual to be true.
TWW: Myths and legends of an ancient kingdom at the bottom of the sea and some old relic remembered only as the "Triumph Forks" all are proven to be true when the King of Red Lions brings Link (and later both he and Tetra) to the undersea kingdom of Hyrule and reveals the existences of the Triforce of Wisdom and the shattered Triforce of Courage upon revealing his own true identity as Daphnes Nohansen Hyrule, the last king of the undersea kingdom.
FSA: Tales tell of a Dark Tribe that once invaded Hyrule back in ancient times before they were sealed away using an enchanted mirror. Remnants and relics of this tribe of darkness are discovered over the course of the game, such as the Dark Mirror and the Trident. The Temple of Darkness is also an eerily mysterious place filled with dark power, and is where the Dark Mirror was placed, suggesting it too may have once had some ties to this ancient Dark Tribe.
TMC: The game opens with a legend of the Picori who once gifted a Hero of Men the Picori Blade and the Light Force. The Picori are revealed to be the Minish, the Picori Blade becomes the Four Sword, and the Light Force is discovered to have been inherited by Princess Zelda, making everything from that legend all true.
TP: Shad and Rusl speak of legends about an ancient sky people who were the founders of Hyrule and left the surface back to the sky where they built a great City in the Sky. Link discovers many relics of these sky people, such as the Dominion Rod, the Owl Statues, the Ancient Sky Book, and a large cannon that launches up to the City of the Sky, revealing that these ancient Sky People really did exist (and meets their creepy-looking chicken-bodied descendants).
ST: Niko tells of a legend from the earliest people of the land the game is set in, about an ancient Demon King named Malladus who warred against the god of this land before being sealed away by said god. The Tower of Spirits is revealed to be the cork of this seal placed on Malladus, who is ultimately revived at the end of the game, revealing his legend to be true.
SS: The war between Goddess Hylia and the Demon King Demise is told in the form of an ancient legend at the beginning of the game. Zelda discovers that she is the mortal reincarnation of Hylia while Demise is proven to be real by his repeated revivals as the Imprisoned before Ghirahim revives him properly at the end of the game.
ALBW: The events of ALTTP are described as legend in portraits found in Hyrule Castle. They are proven to be more than just legend when Yuga brings back Ganon in the flesh (before immediately fusing with him), revealing to all that he really did exist.
And I'm sure there are many more examples but you get my point.