That’s a pretty good idea, wildtabbykat!
I always figured–especially given the existence of the Gelel Empire–that chakra overlayed the previous magic-like system instead of introducing a brand new thing entirely, and that natural chakra was either a thing that you could or couldn’t use. Like you can’t just be taught and train in it if you don’t have the initial ability.
Like… I guess the easiest way to explain would be… I’ve read a couple of HPxNaruto crossovers and to mash up the terminology: Everyone, even Muggles, have chakra but the ability to use NATURAL chakra is for those who would be considered witches/wizards in the HP world. It’s just something you’re born with?
The various clans/blood limits (except for Juugo’s whose blood limit involves natural chakra) are independent of use natural chakra. It’s why not just anyone and their pet dog can become a Sage? Like… why are Orochimaru and Jiraiya sages, but Tsunade isn’t? I can’t really see any of the clans keeping their Sage knowledge to themselves if it is a matter of bloodline.
The Gelel thing is probably… the reason why so many of the Gelel fighters were surprised that the people of the Elemental Nations were putting up a decent defense is that chakra didn’t exist then. So before the Sage of Six Paths, the shinobi abilities would have been limited to the “magic-users” who are (if we’re still using HP standards) a significantly smaller part of the population.
Shikako being able to hear/activate the Gelel stone is because she’s the equivalent of a muggleborn when it comes to natural chakra (or maybe a half-blood? I dunno about Yoshino) whereas if Shikamaru touched it, it wouldn’t have done anything. It would’ve also done something if Naruto had touched it (I’m unsure if the Uzumaki vitality was something like a more stable version of Juugo’s clan’s blood limit, which would make Tsunade a squib in that case).
But then again, aren’t most of the Konoha bloodlines descended from the Sage of Six Paths anyway? Maybe after so many generations they’ve cultivated a blood limit, but lost the ability to use natural chakra and are all borderline squibs?
Then, since Shikako is heading to the Fire Temple to learn how to use natural chakra, the temple is a bit like Hogwarts meets Jedi Order? They probably don’t have jurisdiction in Konoha itself (which is why Team Seven flew under the radar) but maybe the monks travel around and gather possible sages to train them properly?