I figure I'd go on and post some of my findings here
Comparing 2006 tail light wiring to 2008, all the wiring and electronics are identical except there is no "brake lamp switch output" wire on the 08's. Otherwise everything is identical. Pins, connectors, TIPM pin number, everything.
Also, the wiring for a 2006 chassis cab is the same as the 08's (no brake lamp switch output wire) so it's all most likely handled inside the computer
It's probably a shot in the dark but I'm gonna look into the "Combined rear lighting" option in AlfaOBD and see if I can get it to work. A mistake I made before is that I was looking at both outputs when I should've been just looking at the turn signal lamps. If those start showing brake lights, it works perfectly
Even if all this turns out to be true, this would probably be a 2006-only thing. I'm guessing the wiring for 02-05's are similar, but changing the settings in the truck's computer is a whole different story