Edit: I just watched the YouTube video posted below. Looks like we're just dealing with a flawed system.
This method absolutely works.
My luggage is a very large pelican case.
> I'd imagine you need to check-in in a different area and not the front desk?
Yes, and at some airports you get your very own line (which is almost never busy). I've saved multiple hours at certain major airports because of the separate screening procedures/lines.
Most of the time, though, you'll just go to a normal desk, say "I need a firearms declaration," and they'll check you in as-normal, until your bag needs to be screened. At that point, you'll go to another area, unlock the bag for the TSA (if it alarms) and receive a hand-screening.
More info: http://deviating.net/firearms/packing/