The Warp Ammo 4 setup does more damage to armor than AP 4. I don't know what calculation you are using, but AP4 is only a 50% bonus whereas WA4 is 60%. It comes out to around 75 damage per shot v armor extra in favor of WA4. The number varies slightly depending on if you use spare clips or go Shredder / HVB. If you do the latter you have 1.8m penetration which should be sufficient to double hit Banshees and can also easily double hit Atlases. Whether or not there is a lot of cover you need to shoot through will depend on a host of things.
WA4 also has a bonus to Barriers, which you wouldn't get with AP4, and if you end up with any biotics on the team you will end up way ahead (100% prime bonus).
Drill 3 has a small 30% damage bonus and I guess is fine if you are out of AP4.
Not that AP is a bad choice or anything, I just don't see how it is hands down the best choice. I run it on the Crusader in some circumstances, mostly on characters where I am running two guns and the other benefits a great deal from AP (like Crusader / PPR loadouts on GTS or Destroyer).