KK9494
Correction: every human on that planet now has chakra. When the world tree bloomed, it captured every human on earth, including civilians, non-ninjas, and people not from shinobi heritage. The tree aimed to take back chakra from humans. It wouldn’t aim for people who didn’t have chakra. Therefore, every human had chakra.
I like your atp theory and how you actually tried to describe what chakra is but it just doesn't work. If your explanation was right then everyone would have more or less the same amount of chakra. Even if ninjas somehow evolved to create more atp and store it there's no way that could possibly account for chakra monsters like kisame and the first hokage. I don't mean to discourage you because you actually took the time to try to science it out, but the theory just doesn't work at all. Honestly the explanation in naruto doesn't work well either because chakra can be given. Anyways you're trying to use our current understanding of the human body to describe metaphysics which just doesn't work and the deeper you go the worse it will get. Chakra amount is determined by the strength of one's soul and the vitality In their body and that's not something that can be described in the science we currently understand.
Clarification: chakra wasn’t always passed down from just breeding. Please recall that the Sage of 6 paths and his sons taught Ninshu. They were able to pass chakra to other humans. It didn’t create genetic differences in the recipients of the chakra. It took hundreds of years before these adaptations took place. Why are you making up so much stuff?