Are you dialing for position or for angle? You can get a point at the muzzle and breech to be perfectly in line relative to the spindle axis if you want. That doesn't mean that the bore is spinning true with the spindle.
Imagine a slightly curved section of road. Do you point your car to the end point, or do you follow the road as it bends? That's kind of the thought process as to why most guys axially align the first several inches of the breech to the spindle bore. The idea is that you accept that the barrel has some bend in it, and you align your chamber tangent to that curve.
Regardless, we're talking about angles that are stupid small. My guess is someone could clock the bend to TDC, and the next barrel to 3 oclock, and you couldn't shoot them and tell the difference. I say that because I know some shops clock them, and some don't, and I've never heard anybody complain from the shops that don't.