Having been a licensee once upon a time, the bolded part is right up my alley.
There's a researcher up at UC Davis by the name of Garen Wintemute who wrote a paper - Ring of Fire, handgun makers of Southern California:
http://www.ucdmc.ucdavis.edu/vprp/pdf/RingofFire1994.pdf
In which he describes the manufacturers making inexpensive handguns - he documented the internal problems associated with employee theft and the diversion of stolen firearms to the illegal market.
What came out of his report among other things, was the closing of some of these manufacturers due to loss of license for failure to properly document inventory and having an effective security SOP for inventory control.
Here's the thing - ATF has -0- qualms about shutting down any licensee whether it's a manufacturer, distributor or retail dealer for failure to maintain inventory control over the firearms they have in possession - if the manufacturer et al has the financial ability to fight the ATF's administrative action against them is another issue, but I can assure you that in this day and age no licensee in the chain from manufacturer to dealer is losing thousands, hundreds or tens of firearms w/o being on the receiving end of an ATF enforcement action.
How serious is ATF? I know they've gone into retail dealers and compared inventory sales and 4473's going back decades looking for problems.
Here's a local dealer that fought for years, ended up surrendering his license, and in 2006, ATF was looking at records going back to
1967:
http://www.sfgate.com/bayarea/article/SAN-LEANDRO-Big-gun-dealer-fighting-ATF-2500366.php
I did business with Tony for years, never saw anything questionable ever, and they were certainly the highest volume dealer on the west coast - they had so much pull with manufacturers that when we had the SOT we'd often buy firearms from him because his retail prices were lower than the best wholesale prices we could get direct from the manufacturer.
In his case, many if not all of the "missing" firearms were a result of in store paperwork being misfiled or lost, and when the article references that many of the firearms missing were actually in the hands of LEO's, I can testify that this was true, because I was one of 'em.
It's my opinion that the greatest source of stolen firearms is in-transit theft, and like some other laws pertaining to firearms, it seems to me that when the thieves are apprehended, they don't face serious enough consequences.