Are you one of the people that draft these rules??
Perhaps my post wasn't clear enough.
My friend was pulled over because the box hadn't been checked in at the special box check in counter or whatever it is called. The contents were irrelevant.
My own experience with my own box (on a different day / plane) was not dissimilar - just checking it in as baggage was NOT an option, it had to be carted halfway across the airport and i had to sign a dozen forms and have some security ape grill me...my other suitcases were just labelled and taken on board at the counter.
The BOX got special treatment. My question is why? Same person checking it in, same ticket, same aircraft, same (or similar) underpants in the box and suitcase....
As an aside, and to your conclusion re. "Bringing down a plane"... warnings about "did you pack this yourself sir?" have more to do with contraband than counter terrorism.