What I was taught and it does make sense to me(not saying I'm right): When new gears are set up, the ring and pinion have to 'learn' each other. Every single gear setup is different from another. There are manufacturing high/low spots, the backlash specification is a range, it is not a single #, pinion depth is rarely the same depending on the tech, so when gears mesh, they develop a pattern. This is why if you remove gears later to make repairs, it is near impossible to get them back in the same position and can result in noise after repairs if the gears are re-used. We're talking thousands of an inch here.
So, if your gears are overheated or overloaded (usually due to high speed or heat/towing) they can be damaged during the initial time that the gears are 'learning' each other and will likely stay that way forever. I really do feel/think that some of the break-in procedures are excessive and overkill, but so are a lot of procedures in life because people are stupid and manufacturers want to avoid liability.
As far as new gears from factory, I do not think they are broken in, but I am not for sure. However, most factory vehicles are driven off the lot moderately. Whereas with aftermarket gears, the 2 typical reasons people re-gear are bigger tires (vehicle is being used recreationally), and performance/racing (mustangs/camaros/mopar). Aftermarket gears are almost always going to be used more aggressively.
My :twocents: : If you value your vehicle and have just spent money on a re-gear, take it easy and don't be a jackass.