I don't follow. The bore axis is essentially a 2 dimensional line. The line of sight through a scope is also a 2 dimensional line. These two axis are aligned via the scope rings. If these axis are not aligned then you have a big problem that can't be fixed with any amount of leveling. Now that I think about it, zeroing your scope's windage would account for any misalignment. I don't have any scopes on rifles that are set to zero windage after sighting in.
If I dial a scope that is level to my grip (and the ground) with the both the barrel axis and scope axis aligned, it will go where I dial it. I've accurately dialed distances out to 975 yards with my .308 and I've participated in that Ft. Carson match at ranges from 200 to 600 yards while getting hits congruent to my experience level.
The more I think about it, the more arbitrary alignment between anything other than the scope and the ground is. As you dial elevation, you're also changing the relationship between the bore and sight axis. That's why you can see your bullet trace arc into and out of view in the scope at long distances. You are shooting "over" your line of sight. The only thing that matters is a level scope (in relationship to a "true" perpendicularity to the ground) and an accurate zero, if these are off then your adjustments mean nothing. The ground is our reference for the cross hairs, not the barrel or the buttstock.
To quote Ender's Game: "the enemy's gate is down."
I'm sure this is long winded and rambling. I'm no expert on this stuff, hopefully this link adds some credibility to my method: http://www.scout.com/military/sniper...le-level-scope