As to the claim that the last shot fired out of a magazine is a flyer, consider that cartridges in the magazine provide upward pressure on the forward part of the bolt, contributing to alignment with the bore. Changes in bolt position can cause variations in firing pin impacts with relation to the cartridge rim, hence affecting accuracy.
Examine the relative firing pin impacts of the last shot verses other shots. If there's a difference, consider modifying the firing pin, especially to impact a bit below the roll of the rim, regardless of the last shot fired. Since there's no priming compound at that point, the firing pin strikes will be deeper and more uniform if the top of the firing pin strike is just below that fold.
I learned that trick when accurizing 10-22s and modified my CZ firing pin, as described, and it made a difference in accuracy.