The .45 GAP uses a small pistol primer for the same reason that the .40 S&W does, to prevent the primer from striking the ejector or other component on a medium frame pistol adapted to the cartridge. Most .40's are available in 9mm frames and there was concern that the ejector could possibly contact a live primer when ejecting a loaded round from the chamber, or that the primer could be struck by the rib on the bottom of the slide when chambering. In either case an OOB discharge could result.
The GAP is also available in the medium (G17) frame also and that would necessitate a small pistol primer for the same reason. So don't use shortened ACP brass.