If the thread are cut concentric to the bore of the rifle, and the threads on the brake were cut concentric to the bore of the brake, (as both should have been) then the threads are what is keeping everything aligned.
By sanding or not having the back of the brake square to the shoulder on the barrel, you can cause misalignment of the bore of the brake only to the amount of clearance in the threads, BUT the longer the brake is, the more it will show up.
The rule of thumb is, .017 per inch per degree. In other words, is your brake were out of alignment 1 degree from the center line of the bore of both the barrel and the brake, and the brake was 2" long, it would be out by .034" (.017x2=.034")
