Here's
another thread that suggests the unconnected wires mentioned in the manual lead to the under-dash pigtail meant to connect to an aftermarket brake controller.
With the OE controller, any reasonable person would expect it to be functional as delivered. If that's not the case, I wouldn't hesitate in raising hell with the dealer and for damn sure wouldn't pay anything for them to make it operational. You already paid for that option when you bought the truck.