Kl will have a look, (reserve this space

)
Edit:
Ok read through it, mind = blown over vestigial eye inside my brain first of all. Yes it might just be retina that can react to light but still that's pretty unusual, something I didn't know. Ergo its a vestigial eye by default.
Revisited: Where did Chakra Come From
But about what you said about chakra, that people didn't "know" how to use it, I have to disagree Madara has just stated how it is the Sage planned to solve wars and create peace, through chakra. He shared his chakra with everyone allowing them to kneed their own mental and physical energies. This means that his chakra allowed them to mix their own energies to create their own chakra. Its almost like his chakra became a chakra network for them like they have a miniature mokuton bonzi tree inside them lol.
To me this statement by Madara is pretty explicit on what it means.
Regarding there being chakra BEFORE the sage I agree completely. The summons likely used Senjutsu exclusively. Ergo Kaguya was the first HUMAN to wield chakra.
The Third Eye
I agree, overall best explanation of where the Byakugan came from and how over the generations a Dojutsu can be trained and then inherited. I would rep you 10 times over for this analysis but I can't.
Edit:
Just reped every random-er in this thread still can't rep you T_T