Once you have the powder charge that nets the best ES/SD you can vary the seating depth to allow the bullet to exit the barrel at the optimum barrel time. (time were the barrel end is at an optimum point in it's vibration)
If you play with the Optimal Charge Weight method of load development you will be able to see a figure eight pattern in the groupings where the barrel whips in that pattern. Usually the top most crest of the figure eight is a good point to start playing with seating depth. Coincidently, this also, many times, coincides with a great ES/SD load.
It is a very similar, if not the same, concept as barrel tuners. With the tuner, you tune the barrel to allow the exit of the bullet at the optimum point. With seat depth, you tune the load to exit at the optimum point of barrel harmonics.