The general rule of thumb for mounting a scope is to have it as close to the boreline as possible. Gale mentioned some of the limitations including clearance for the objective bell and drop of stock. Clearance must also be had for operation of the bolt handle.
The issue of closeness to the boreline comes into play when one shoots at distances other than what the rifle has been zeroed in for. A scope mounted high above the boreline (like on the carrying handle of an AR15/M16) requires the bullet to exit the bore at a substantial angle for it to intersect the scope's line of sight. While this is no problem at the sighted in range, when the shooter wishes to engage a target at longer distances, the bullet will impact over the point of aim.
For instance, an handle mounted scoped AR sighted in for 50 yards will shoot 3.6" over POI at 100 yards. At 150 yards, 6.1". At 200 yards, 7 1/2". Similarly, a scoped flattop AR (2" above boreline) sighted in for 50 yards will shoot 1.1" high at 100 yards and about the same for 150 yards, and .1" low for 200 yards.
On a rifle with a high mounted scope, the shooter must do more trajectory calculations when engaging targets at a distance greater than the zeroed in distance. It's simply faster to do those calculations on a lower mounted scope.
I think I read this info in the Ultimate Sniper, or from Mike Lau or Dave Lauck (both of whom are custom rifle builders).
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