My guess is the idea of Ganondorf being separated pretty heavily from Demise was something they didn't originally intend(an idea created for TOTK), so the worst that happened is the Rito/Zora change, but it's not like the species couldn't split again anyway. Gorons were nearly gone throughout WW thanks to the Goddesses flooding it(and they also killed off all Gerudo that way), but clearly they're all fully alive and back as of BOTW.
It's also possible that the timelines simply combined because consistency doesn't matter. There's honestly more than one way it could go. I wouldn't be surprised if they have a new book coming out later. More and more games are coming out. There is no new actual guide of any sort, so. Just minor statements.
Though it is worth noting that Ganondorf is separated from the Triforce entirely in WW, so BOTW Ganondorf having no connection to the Triforce is easier to justify as he canonically lost his connection to Demise in one story. But reincarnation is supposed to be because of Demise, so who knows. They could just as easily resurrect Ganondorf in WW since he's nothing but stone, and he'd be logical as a different person too. Though stone didn't stop Ganondorf from reincarnating in Four Swords Adventures, so it's not like that matters much on its own(though as noted, Ganondorf can no longer be resurrected by Demise's normal reincarnation cycle in WW, at least apparently, because he lost his connection to him. That doesn't mean something else can't cause it, etc.)
On another note, I hope we see another take on Ganondorf. There's a lot of neat ideas throughout other fictions(like the OOT Abridged) as well as WW somewhat trying to give him less evil traits that it's much easier to justify non-completely evil versions without much hassle. That, and if you don't include Demise, he has way more agency to do what he wants. I never liked Demise since him being responsible for the whole cycle of evil and reincarnation(in general) makes many villains less likely to have proper agency. It makes OOT Ganondorf being a badass conqueror feel more like a "was he roped into this? Corrupted? How much is it Koume and Kotake's influence and not Demise's?" I liked the idea the witches taught him to be evil, since at least he chose to embrace the evil on his own merits. It made WW where he saw how he went wrong feel an angle worth exploring. Now, uh... the impact is lost cause of a lack of agency to a degree.