My belief? The whole 'Chakra-Granting Fruit' thing is a myth, or an allegory. It's not what really, honestly happened.
Maybe the Six-Paths Sage's mom was just the first person to figure out how to access and harness her chakra (which, as established earlier in the manga, is the present-in-all-things power made from a person's physical and mental energy), and her son was the first scholar of chakra and used what he learned to become the Sage.
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