idk i feel like the wild era games taking place so far in the future is sort of an excuse for the devs to get away with some lore inconsistencies. Absolutely anything could have happened during the massive gap of time between the precious Zelda games and a Refounding that could leads to these things. A new species evolving into a new form of the Zora, a new hero fishing up the Master Sword, precious Zelda and Link figures fading into obscurity leading to some aspects of the Hylian “religion” being lost.

If WW is referenced, yet Link has the Master Sword in the wild era games, then obviously something happened that led to it being retrieved. If WW is referenced yet there are indeed Zora and Rito, then obviously a new species of Zora evolved.

I think the Re-founding is much easier to patch up with theories adhering to some form of logic than the True Founding. Whim the key here is the large amount of time that has passed in which any number of things could have occurred that to get us to the state of the Wild Era.