I wouldn't carve holes in the padding, the CFR (Code of Federal Regulations) where it is pretty much carved in stone, even if it does suffer from interpretation by the unknowing (TSA types among them,) states that ammunition needs to be an a wood, fiber, or metal...WAIT!!! let me look it up and post it again...or didn't I already post it?
From 49CFR175(A)(5)
(5) Small-arms ammunition for personal use carried by a crewmember or passenger in his baggage (excluding carry-on baggage) if securely packed in fiber, wood or metal boxes, or other packagings specifically designed to carry small amounts of ammunition.
Anyway, the gun case's foam liner is not designed to carry ammunition, even it's carved up, so an overenthusiastic TSA screener is likely to see to it that you "voluntarily surrender" the ammo at a minimum. The case is not "designed", in the strictest sense of the term, to carry ammo. The safest thing would be, if you must carry less than a full box (and even partial boxes fit in the rule above) to get a target block like someone mentioned earlier, something that is obviously designed to hold ammo and fits under the "other packagings" portion (plastic.)
We had quite a discussion about this when a duck hunter came through with a bandolier in his bag, with about 30 rounds of shotgun shells in it. We came to the conclusion that the bandolier was fiber and designed to carry ammo, and was pretty secure in the way ir was rolled and wrapped. Whether this conclusion would have been reached by TSA people with less of a sense of humor (or ridiculous or sublime) is subject to conjecture.
There is nothing in the CFR that says primers must be protected, it says the ammo must be securely packed in an ammo container. This has also led to much debate about loaded magazines (one screener opined that a loaded magazine was equivalent to a loaded gun, even if the mag was well separated from the gun, not all of us are knowledgeable or even common sensical) and the conclusion was that although magazines are designed to carry ammo, to do so securely they must either be in a magazine holder or in a gun, otherwise rounds can and do pop out (the voice of experience here if nothin else, loose mags in pockets can lose rounds.) The consensus was that if a magazine with rounds came through our area, and it was in a mag holder that fastened closed ie a LEO type, then it would be acceptable, but not in open top puoches, such as what I carry. You can't win them all.
Educating people to the difference between magazines and clips has also been fun, but I did win a concession that a bandolier of Garand clips (loaded) would have to be considered: fiber and metal; secure; and a packaging designed to carry small amounts of ammo (at eight rounds per CLIP.)
And I must reiterate, this applies only to conditions that existed at the time and place of the discussion and may not apply when you have your butt in a wringer because you decided to push the edge of the envelope.
There is a lot of interesting reading in the CFR, and Chas can tell you that a lot of it is about as clear as mud, but just about every scenario concerning checking firearms and ammo in baggage is covered, and it only take a few words.
Me, the next time I fly with a gun, my ammo is going in a .223 ammo box, the sturdy military model, in boxes of its own. The last time I flew some screener got in my bag and emptied out my ammo boxes, so all I had was empty boxes when I got where I was going. I do have to admit that I was a screener myself at the time and that they did send my ammo, in another box. They also wrapped my bag in about 50 yards of Saran wrap, but I knew about that trick and had a sharp knife easily accessible in a side pocket so I was able to cut it free. You should have seen my sirprise when I got to my rental car and started to strap up, only to find my ammo boxes empty.
For further reference, 49CFR1544.203f is included here.
(f) Firearms in checked baggage. No aircraft operator may knowingly permit any person to transport in checked baggage:
(1) Any loaded firearm(s).
(2) Any unloaded firearm(s) unless—
(i) The passenger declares to the aircraft operator, either orally or in writing before checking the baggage that any firearm carried in the baggage is unloaded;
(ii) The firearm is carried in a hard-sided container;
(iii) The container in which it is carried is locked, and only the individual checking the baggage retains the key or combination; and
(iv) The checked baggage containing the firearm is carried in an area that is inaccessible to passengers, and is not carried in the flightcrew compartment,.
(3) Any unauthorized explosive or incendiary.
(g) Ammunition. This section does not prohibit the carriage of ammunition in checked baggage or in the same container as a firearm. Title 49 CFR part 175 provides additional requirements governing carriage of ammunition on aircraft.
And I am still working on my "comprehensive" "Jim's handy guide to flying with your gun in checked baggage to avoid unnecessary delays and other discomfort including chats with the Transportation Security Administration and Law Enforcement Officers."
I hope that title isn't too unwieldy, I expect to be paid by the letter.