1) If you spend 15 karma (or 30 karma post-chargen!) to add -6 AP to one specific light pistol, more power to you.
2) when combining with 2nd order effects like APDS and Bullseye, remember the GM says how the rules interact, not the Player. That called shot increases the base AP. It doesn't factor in APDS, and if you don't want it to it doesn't have to factor in Special Modifications, either.
3) Prototype Materials explicitly calls out that it requires GM permission. If stacking everything towards AP is an issue for you, don't give permission to Prototype Materials unless they spend the improvement on something other than AP.