Greg,
The external ballistics program is just spitting out the effect of muzzle velocity variations, not all the other factors that cause dispersion. If you are getting vertical down to 0.5", then you are in a good position to recognize the effects of additional vertical caused by intentionally varying muzzle velocity. Measure muzzle velocity of each shot with a chronograph and measure the elevation of each bullet hole on the target. Plot a graph of elevation versus muzzle velocity. This is the ladder test that has been discussed a number of times. What you want to find is a spot of the 300 yard graph where elevation decreases at a rate of 0.44" per 20 fps increase in muzzle velocity to eliminate vertical at 600 due to this one source of vertical dispersion. If the first graph doesn't have such a spot, then there are many ways of changing the shape of the plot, including barrel and stock stiffness, weight distribution of the rifle and how the rifle is supported on the rests.
Yes, the optimum load/tune is different for each yardage. For instance, for a 1000 yard zero and the same bullets with 20 fps ES, the slow bullet must strike about 1.4" higher at 300.
Cheers,
Keith