I keep forgetting about the Fokka! I think most people do. Do you think Fokka could a subset of the Rito, rather than a cousin,or precursor species?
You mean like a hammer and chisel?
Not really. When talking about it, the people who would be in the know don't even acknowledge it as a thing that exists. She isn't told to keep it a secret. Nobody tells her that there are myths that sound kind of like it. The idea of what the Master Sword is seems completely new to everyone. Everyone.
And, Zelda would know exactly where it would be kept. Taking the sword to the pedestal, and attempting something there isn't even a thought. She doesn't even try pouring what power she can into the blade that would be hidden away, in hopes that it wouldn't have shattered in the first place. Strengthening the blade before hand would have had the same effect, as far as the timeline, due to it being a closed loop. (Narrativly, there would barely be a game, though.)
There are numerous holy locations, that she knows about, modern day, and yet using her own body was her go to solution. Either she panicked, and did the most immediate, and risky, thing, without thinking about alternatives (which is not supported by the narrative); or she knew that these locations did not exist yet, and sacrificed her self knowing there was no other option.
Except that it provides none of the pieces that are missing. (I can provide the list again, but it's getting a little old. I do plan on laying out all of my thoughts in a future theory post. I will be sure to include a full up to date list then.)
As far as refounding through an off screen kingdom collapse, The prologue for SS is that collapse.
With the physiological differences between the Rito we see now, and the ones from WW, we don't need the same group to evolve twice. they are two separate types, that share the same name. The Rito we see now could have evolved long before the flood, then the Zora could have been changed to join the existing Rito. Alternatively, it has been pointed out that there is a lot of cross species coupling in the Zelda universe (mostly with Hylian partners, I might add). The Zora may have coupled with the Zora so their children would be Rito, and therefore safe from the flood. One thing we do know, is the Rito Legend of the Storm Ark does place Rito history before the Cloud Barrier.
(I still think there were Zora who were not saved from the flood, who became the Fishmen.)
Having a Ganondorf before OoT is the only real issue, except that no game actually states that he is the first. If anything, the game tells us the whole one Gerudo male every once in a great many years becoming king, which leaves the door open for others before him.