I'm a happy GAP owner, too, and bought a G39 last year (got tired of waiting for Gen4). Here is how I understand the short barrel velocity issue. Most ammo companies load their .45 ACP and GAP ammo to the same power levels. The GAP functions at significantly higher pressure due to the shorter case and other design differences. GAP will generally out-perform ACP given identical bullet weights and barrels of equal length. The velocity and energy difference is marginal, maybe 5% at best. ACP in +P beats the pants off GAP, though. No contest. GAP has no +p equivalent.
I hope this answers your question. I'm not a ballistics expert, but I do see that GAP, particularly the G39, as being a winner in terms of size/handling/performance.
Glock 17, 19, 21SF, 26, 37, 39
Glock Advanced Armorer (AA), Glock Instructor Workshop (IW)
Remington 870, Benelli M1, Smith & Wesson 3000, Mossberg 500