You could be carrying a case with "THIS IS AN IED" spraypainted on it in bright pink, and most people wouldn't pay attention to it. Most people don't even know what molle is, on top of that. A lot of guys forget that not everybody is a gun guy.
That being said, if you're serious about a "covert" case, go to Goodwill and buy a used bag of some sort. I bought a zip up bag that was made for a fold up chair, and lined it with foam.
I recommend highly against tool bags/boxes, instrument cases or ones marked with well known name brands. Guns aren't the only valuable things that can get stolen. Hell, if I was a thief, I'd be much more inclined to steal a DeWalt bag than a gun case; tools and musical instruments are still pretty valuable and much easier to sell than stolen guns.