I think what it is is that people decided to "experiment", and try their barrels from different rifles to fit on other recievers that they might have. While the tolerences aren't 100% true from rifle to rifle, they are pretty close. Most people are taking their chances on getting a barrel they buy to lock up with the proper headspace on their reciever. It might void their warranty, but like you said, it might be the need to get a new barrel w/o waiting for the factory, the new fitting charge, or that the company is worried about lawsuits, and puts that disclaimer in to cover their butts....who knows? But needless to say, yes it's the same procedure as before w/ the factory, people are just taking matters in their own hands.
~~~Cattleskinner