It's pretty simple, really. It's all about the Physics. Harmonics are very unpredictable. Why do you think that musical instruments that are made by the same person using the same materials and techniques from the same source at the same time can still end up being different?
No black magic involved. Even when made from the same batch of steel at virtually the same time two barrels may have enough of a difference at the molecular level to have different harmonics once they are used.
One of the factors that define the accuracy of a rifle/ammo combination is where the muzzle is in when the bullet exits. A barrel will "whip" when hit with a hammer or when a cartridge is ignited. If a projectile leaves that barrel at the close to the same point of its "whipping" action, the you may very well have an accurate match.
There is also the possibility that the barrels' twist is not exact. Some 1:9-inch twist ARs loves 75-grain bullets because they are closer to a 1:8.5-inch twist. While some, even from the same lot, may only prefer a maximum bullet weight of 69-grains.
One of these factors is how sharp a cutting tools stays between barrels. There is bound to be some loss of sharpness with each use and this may be enough to make the difference.
Of course, I could be full of crap and someone will eventually come along to correct me (it wouldn't be the first time).

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