I'll start by saying that I'm no target shooter and MOA, although I know and understand it from an engineering point of view, really doesn't come too much into play for me. Personally, I feel the barrel breakin process work on two principles.
1. Understandably if you have a rough factory barrel the repeating of the process as others have described is going to help reduce any errors in the consistancy of your accuracy.
2. If your shooting and cleaning a whole bunch over the course of a few hours on the bench or even over a few days then you're constantly learning your rifle. A person seeking the type of accuracy a lot of the people in here are seeking needs that time. Remember that both your rifle and you are partners.
As far as how many shots it takes and all that to break in a rifle. Well its really just a study of friction. I think it definately takes more than a hundred shots or two hundred shots to break in a rifle. Eventually, unless you can figure out someway to eliminate the friction factor (which is impossible based on the concept of rifling) the precision of your accuracy is going to be ever changing. Personally, I have many rifles and my two best shooters are a 22 that my grandfather bought the day before pearl harbor was bombed and a 308 savage I bought with a heavy barrel. The 308 is pretty easy to understand why its accurate but the 22 is a prime example of how pure quality materials will withstand corrosive tendancies more easily than the flawed materials often used today. In other words they just don't make'm like they used to.