Having an idea of how the reamer works can allow one to correct a misaligned chamber to a certain extent. The things is, even a close fitting pilot will have SOME clearance (usually on the order of .0001" radially or so) and there is also some clearance between the floating pilot and the reamer (another tenth, perhaps). On top of this, there is the potential for a bit of flex. When approximately 3/4 inch of the reamer body is cutting, the forces on the body can over ride the pilot. The body of the reamer tends to cut to the center of the existing hole so if one wants the throat of the chamber to be concentric, the reamer body has to have a start which is concentric to the bore at the throat.
In the case of the 250 AI to which Mule Deer alluded, the original chamber may well have been concentric at the throat but may have been misaligned so that the base was not perfectly concentric with the throat. When the gunsmith rechambered with the AI reamer, the body of the reamer was influenced by the body of the chamber and the pilot may not have even been in contact yet. With an eccentric start, the reamer produced an eccentric throat.
So, how could he have avoided this? The best way would have been to indicate the throat of the original chamber so that it ran at "zero". Then, if the chamber was running eccentric at the base (and it probably was), he should have used a boring bar to true up the chamber to within about .005" of the diameter of the AI reamer at the shoulder. It would not even have been necessary to bore the whole body; an inch or so would have been more than sufficient. Now, with a good, concentric start, the reamer would have cut a good, concentric throat.
Of course, one has to be a little careful with this boring bar stuff too. On another memorable job I miscalculated the angle and roughed out perfect 308 Norma chamber. Perfect that is except for a ring up near the shoulder where I had bored a little too big and left a groove about .002" deep. This is another barrel which resides under the bench and one which cost me a new barrel (it's a wonder I ever made any money!). I never even noticed the flaw until I tested the rifle.
As MD mentioned, an eccentric chamber can shoot amazingly well. About thirty years ago, I had occasion to fit a very crooked Bauska barrel to a mauser action. This barrel was more than a little curved and I, quite frankly, did not have the knowledge to deal with it at the time. I did the best I could but the throat was visibly eccentric. Not by much; probably about a half thou. Still, I didn't think much of it and told the owner so. The thing was, that rifle (a 6.5/06) shot! He showed me a bunch of two hundred yard five shot groups which hovered around an inch and a quarter. Not half bad for a lightweight sporter. So you never know. GD