So Chakra manipulation is hereditary, civilians can give birth to ninja, but ninjas together don't having civilian kids. Are there enough ninja-civilian kids to make any observations there? Sounds like within 20 generations or something, all humans will be Chakra humans (or dead). I suggest we do literally nothing with this knowledge, but it is interesting. I wonder if someone will one day be able to give their Chakra capacity onto a civilian 18 generations from now...
Maybe Chakra has a negative impact on fertility? I mean, as far as Hazou knows
(and for all we know, it's the truth) the Sage gave it to humans. So it wasn't part of our natural evolution. So who knows
what it could be doing to the human body. Granted, it's been countless generations since then, so evolution would likely play a hand at stacking the deck towards in humanity's favor.
Anyway, it could be that minor amounts
(civi to genin) don't really do anything, but then once you get to the upper tiers
(chuunin to jonin) you start seeing some abnormalities
(bodily, mental, spiritual) that give jonin their eccentric reputation. And once you get into S-class, Kage, and Jinchuuriki levels? Well, they're not exactly shining bastions of human stability. And almost all of the stronger ninja die really, really young --meaning we don't really get to see the longer-term effects of high amounts of chakra on a person.
Of course, that's assuming that Chakra runs on such feeble things like "logic" and "reason." The Naruto universe has a Soft Magic System and though it
can be understood to a degree, it's still an inherently mysterious thing that doesn't conform to hard rules. And it seems like MfD is following that trend.
So for all we know, Chakra might be like magic in
Harry Potter, where it might vanish from children with no apparent cause, creating a chakra-squib. It might be that Chakra metaphysically "calls" to Chakra --meaning that a ninja is far more apt to marry a fellow ninja, or that ninja-civilian pairing result in Ninja-capable children more often than should be mathematically possible. Or it could be that fetuses that develop around high amounts of ambient Chakra --such as in ninja villages or particularly...
wild places in nature --are born with more active coils. Or it could be that celestial bodies such as the stars and the moon have an influence
(we don't know if the moon is really the moon or if the stars are really the stars in MfD's iteration of Naruto. Could be tears through our reality and into the Out for all we know. Or the eyes of the hive mind looking down on the EN).
It's a little like Tolkien's magic system in that, although the readers know some stuff about magic, it's often never really all that much.
Who knows? Not us and certainly not Hazou. And I doubt that even Orochimaru really knows. I doubt that he's really care about the more metaphysical/ontological philosophy relating to Chakra. His area of interest --if MfD's iteration hasn't changed this --is practical research and, specifically, physiology/anatomy/biology and bloodlines.