OK, on the assumption that rougher/finisher cuts a very good chamber, here's part B.
Let's assume you are willing to cut the chamber before cutting the tenon and threading it and cutting the shoulder. Let's assume too that the shank of the reamer -- the opposite end of the bushing -- is ground, or if not, you could specify that it be ground.
When you indicate the barrel in at first, as exactly as you want, you haven't (likely) picked the exact spot where he pilot bushing will fall after the chamber is cut. So, as you make the last pass with the finish reamer, leave it in, and check things by running the dial indicator on the reamer shank. If it shows runout, re-indicate the barrel using the reamer shank. Then cut and thread the tenon and shoulder. Now the chamber end of the barrel will be square to the case head.
Actually, using his slightly different approach, I think this is essentially what Gordy is doing. The only difference is he's "pre-indicating" based on two points at the chamber end of the barrel, points selected about where the bullet will be. He's essentially splitting any error between the chamber and the shoulder. As Phil (& others) have pointed out, we're not talking large numbers here.