My midnight edition did not come as a trail boss, however I purchased it all later and installed it myself (at a nice discount at the dealer). After many questions and compiling several different schematics I was able to wire the thing up. Your dealership failed to 1) remove the cab mounted brake lights, and probably 2) Correctly install the wiring harness that goes to the distribution box under the hood. The top of it must be disassembed and the CHMSL wire must be tapped to make the 3rd brake light work. During my install I asked the Chevrolet dealer questions.... they had a deer in the headlight look, and upon reading the schematics they really wanted nothing to do with it. There will be a wiring harness that runs along the frame rail on the drivers side, it will run up to the distribution box under the hood. The ground connects behind the fog lights in the fender well (wheel well cover has to be removed/pulled back to get to it), there is a power wire that connects to the M5 screw at the main power of the distribution box, this feeds the constant power to the relay and sends power to the Off road lights when the switch is turned on in the cab, and then there is the wire for your 3rd brake light in this harness that should go to the firewall side of the distribution box and tie in to the CHMSL wire.
Hope this helps, but it sounds like they missed the CHMSL wire.