The rules for each airline are pretty straightforward. You can never go wrong with taking ammo in the factory box (not bulk packs), or in a standard plastic reloading box, and then putting that ammo in a separate case from your guns. I have several small Pelicans that I take when I'm only travelling with pistols... the 1200/1400 models are perfect and will go inside any normal luggage... just remember to put TSA locks on them if they're only carrying ammo and not firearms.
The SOUTHWEST policy actually reads:
Magazines or clips containing ammunition must be securely packaged (placed in another small box or in a secure cutout in the carrying case, in order to protect the primer of the ammunition).
Loose ammunition or loose loaded magazines and/or clips are not allowed.
Ie, if you had put your mags in another "box" (cereal box?) and wrapped them in a t-shirt, AND placed them in with the guns, it would have satisfied the requirement that having them smashed under the foam did not, because if in the same hard-case, you need cutouts in the actual foam... makes no sense at all, but the rules are at least clearly written. Some airlines it's a bit more vague and open to interpretation.
I've flown a bunch with a pair of completely packed Pelican 1720's... and I mean packed. No cutouts for anything... and all my guns, knives, mags, ammo, loaded mags, ammo boxes, cleaning stuff, bipods, etc... all just thrown in with the center foam removed and everything wrapped in t-shirts. I've never once had an issue. However, I think I'm gonna get a bit more organized for my next trip... good excuse to buy a few more cases.
AMERICAN:
Ammunition must be:
In the original packaging from the manufacturer or in packaging specifically designed to carry small amounts of ammunition (made of fiber, wood or metal). Ammunition is not accepted in magazines or clips.
DELTA:
Ammunition must be:
In the original packaging from the manufacturer or in packaging specifically designed to carry small amounts of ammunition (made of fiber, wood or metal). Ammunition is not accepted in magazines or clips.
UNITED:
No more than 11 pounds of ammunition may be carried. The ammunition may be packed in the same container as the firearm or in a separate container. Ammunition must be packed in the manufacturer's original package or securely packed in fiber, wood or metal containers. The ammunition inside the container must be protected against shock and secured against movement.
ALASKA... holy cow, that's pretty specific:
On Alaska Airlines flights 001-999 and flights 2000-2999, up to 50 lbs.(domestic) and 11 lbs. (international - where permitted) may be checked. Customers checking in or connecting to Alaska Airlines flights 3300-3499 are limited to 11 lbs. of ammunition. Ammunition must be securely packed in the original manufacturer's package or in a container designed for ammunition and of sufficient strength to protect it from accidental crushing or discharge (i.e. wood, fiber, plastic, or metal). The projectile must be no larger than 11/16" in diameter, the size of a dime. Ammunition may be checked with or separately from the firearm. Spent ammunition shells will be accepted in checked baggage provided they meet the same acceptance procedures as live ammunition (e.g. packed in a crush-proof case)
JET BLUE:
Ammunition for the firearm cannot be placed in the same container as the firearm, but may be in the same checked bag as long as everything is packaged properly. Ammunition must be housed in a separate container that is completely separate and distinct from the firearms locked box. The ammunition must be packaged in a fiber (such as cardboard), wood or metal box specifically designed for carrying small amounts of ammunition. Ammunition is limited to 11 pounds per customer. Ammunition will not be permitted in carry-on or checked baggage on international flights.
I had to politely tell the painfully new guy I was not LEO, and he started stammering and shaking. A more senior agent took over and things went smoothly after that.