rem40xb1,
it has nothing to do with the quality of your muzzle brakes. Assuming they are perfect, the tolerances on the muzzle brake threads and shoulder can result in the bullet not passing through the baffles perfectly centered. I would never install a pre-drilled muzzle brake on a precision rifle for myself (If someone brings me a muzzle brake predrilled and says to install it, I'll do my best).
but to install a muzzle brake correctly, you must put the barrel in the lathe set up perfectly around the axis, so why not jut bore the brake once you have it threaded and installed. If a brake is predrilled .020 over, I'll go ahead and open it up a few .001". Especially on a low energy round, more centerd is more important than more recoil reduction.
Using a boring bar to pre-drill will do nothing to help. The boring bar is used after install to match the centerline.
I just reinstalled a brake on the new barrel last week and had to open up .004" to get the hole centered. If I hadn't done this, the brake would have slightly deflected each shot.
You should do what your customers ask for, but if I were you I'd recommend that they have the gunsmith who installs them open them up to .020 over.
--Jerry