Is everyone sick of timeline theories? No? I have one that's really out there if you're interested.
The thing is; in Wind Waker, you learn that when Ganon(dorf) returned after being sealed at the end of Ocarina of Time (adult timeline), and there was no Hero of Time to stop him, the people of Hyrule prayed to the gods to stop him; they responded by flooding the entirety of Hyrule to contain Ganondorf.
And, in Majora's Mask, you're helped by a Goddess of Time, who returns Link back in time whenever he plays the Song of Time; letting him keep unique items but removing his rupees/arrows/bombs/etc; my theory for the latter is though she can manipulate time and space a bit, she can't temporally duplicate things, and if she let Link keep his ammo and rupees, he wouldn't be able to find them in the grass again.
That may seem a bit of a non-sequitur, but my idea is this; unwilling to let the majority of Hyrule's population drown with Ganon, Hylia, Din, Farore and Nayru plotted a scheme; either choosing one of Hyrule's multiple parallel dimensions (Sacred Realm, Lorule, Termina, Twilight Realm, etc), or creating a whole new one, they spirited away most of the population of Hyrule before its flooding to another world.
That alternate world is the setting of Breath of the Wild, or rather, was the setting of Breath of the Wild 10,000 years ago; during the events of Wind Waker in Flooded Hyrule, the inhabitants of Wild Hyrule started developing and growing a civilization anew, receiving the occasional refugee from the Great Sea and sending back the occasional sample of their technology (see the Tower of the Gods, essentially an oversized Sheikah Shrine).
When the events of Wind Waker happened, and Ganondorf was stabbed in the head by the Master Sword, he wasn't quite definitely absolutely killed; his spirit along with his dark magic was lured into Wild Hyrule, where another Link, another Zelda, and a large army of Guardians were all waiting to thoroughly kick his butt and seal his spirit away for the next 10,000 years.
Absolutely zany theory, I know. But, think about how frequently it rains in Breath of the Wild. Maybe it's a slight breach of whatever barrier lies between Flooded Hyrule and Wild Hyrule.