I probably should have been more specific by what I meant when I said, "properly stored". I think you can put anything into the hard-sided case with the flaregun as I've heard photographers (as someone else mentioned), musicians, tech enthusiasts, etc will get a pelican case, put their cameras, computers, instruments, etc into the case with the flaregun. You're right that you can't just dump it into a dufflebag and call it a day, and I'm pretty sure I've heard that you can't put a dufflebag inside the container with the flaregun, as I've heard they'll tell you that it needs to be independently checked and stored in the luggage compartment.

To put it another way, the case isn't transporting your clothes, it is transporting your flaregun and you've just happened to use any extra space to pack your clothes.

I flew American Airlines with a gun and it had to be in a hard locked case that I was able to put in my luggage to be checked. I had the keys. I had to pick up my luggage at the help center.

I don’t remember any part of the check in process where I would have been able to put the case back in with the rest of my luggage.

That's odd. I've flown with a pistol several times and it's always been the other way around. After TSA does their check the locked pistol case gets put back inside a piece of my checked luggage. What have they done with yours? Just tossed it on the conveyor belt like its another piece of luggage?