My best guess based on personal observations, would be that regardless of quality control, all firearms have different tolerances, even with in the same model on any given day. Climate and weather can effect even a brand new firearm. And possibly some employees at these firearms factory's have different abilities, attitudes and moods while working. Any of the reasons I have listed could possibly effect the way a firearm functions out of the box.
As for break-in periods... Any part could have an imperfection such as a burr, out of round, not perfectly straight, etc. and once all these minor but safe and workable, often normal imperfections (providing they are with-in tolerances) sometimes need a bit of time and motion to work into a comfortable fit. This is actually true with nearly anything that requires movement to function together.
I recently purchased a Remington M770 bolt action rifle, nice gun but the action was stiff and not terrible smooth out of the box. 60 rounds later it was smooth as glass, later of course I disassembled and did an action job to make it even better. Seems nearly anything mechanical needs a bit of breaking in
