A large part of what makes a person able to shoot a scoped rifle accurately is learning how to deal with that very thing. The farther offset the scope is from the bore, the greater degree of compensation you need to have at close ranges. However, as range increases, that difference diminishes.
Still, even if you could magically line the scope up with the bore, that would only be accurate for a distance of a few feet. Gravity would still operate and be pulling the bullet down, forcing you to have to make adjustments for targets at different ranges. So it's not like having a few inches difference makes a completely new problem, it just changes the math a little.
The bullet is dropping the instant it leaves the barrel so even if it were possible to align the scope with the bore of the rifle, it would only be sighted in for a short distance. Accuracy comes from consistant bullet drop at different ranges and the shooters ability to adjust the scope or hold on the target to ensure that the line of sight and bullet cross paths at the desired windage and distance. Obviously the closer the scope is to the bore of the rifle, the better things are, but a few inches differnence directly above the muzzle at long range is the least of a snipers worries when trying to place a single cold bore shot at an unknown distance on a moving target.
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