But it also states that Skyward Sword Zelda’s descendants founded Hyrule shortly after the sealing of the sacred realm. Skyward Sword Zelda wasn’t a Zonai though.

There's no indication of how much time passed there. It just says that Skyloft came down, and then there was an entire era of chaos, ending by the sealing of the sacred realm, then the founding of Hyrule kingdom, and the beginning of the era of prosperity. The graph even has an extra empty slot between the sky era ending with the return to the surface, and the era of chaos with the sealing of the sacred realm.

Hyrule Historia p. 77 says that "the world became known as Hyrule" and "the Hyliaans, descendants of Hylia, lived in Hyrule" - but the descendants of Hylia are the descendants of Skyward Sword Zelda, who is Hylia incarnated. So we're already talking a few generations there.

Then the legend of the supreme power spreads, and Rauru, the sage of light that we see in OoT, builds the Temple of Time to seal the Triforce and the Sacred Realm.

And then the descendants of the goddess Hylia, reincarnated as princess Zelda (so that's the descendants of SSZelda), established the kingdom of Hyrule, to protect the Triforce. Then after some time, we get to OoT.

The only thing that's changing here with TotK is the imprisoning war. The one we see in TotK and the one we see in the LttP backstory (and also in Hyrule Historia) simply seems to be... not the same event at all. The TotK events are just a different war that is not the one we've known about so far. As for Rauru... the founding of the kingdom and the sealing of the sacred realm did happen in the same time period, and they have the same powers. And the Zonai could easily have had an entire civilization and left between the Skyward Sword ending and the sacred realm sealing.