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.