There's Kokiri in OoT, they transformed
Didn't think this through 100%
That's just the thing. You can't pin BotW down to one timeline, they made sure of that, so I feel you have to get creative to place it. Sure, there's no evidence for HoT Link staying but that doesn't mean it couldn't have...
Alternate universe from OoT: The hero stays.
Link refuses to be sent back by Zelda to live out his childhood. Knowing that Ganon is only sealed away, not destroyed, he and Zelda urge the Sheikah to prepare for his return, prompting the creation of the Divine Beasts and Guardians. Ganon breaks...