Bullet six of your post answers the real question. When you are done with Customs you have to transit a secure area to get to the exit of the airport. Even if you aren't connecting they have baggage service from Customs to the exit of the terminal.
This screening of a passenger that isn't connecting is more an issue with a weird terminal setup than anything else.
Domestically, I've made some amazingly short connections through that airport.
I was emphazing it for the other readers. The key to the issue is that the 'exiting' passenger has free access inside the security area after having access to his checked bags.
I take it that this means that your baggage leaves the secure area right after customs and you go to pick it up somewhere else?