Having worked on repairing several of the Cobalt/Goblin wiring harnesses, My position is "abandon in place"(Insulate with tape and wrap them into the harness) any unused connectors that DF did not have us delete.
As manufactured there are subsystem connectors present in harnesses unused and taped aside; example, in the body harness there is a plug to the Automatic shifter(neutral safety switch) that is present(abandoned in place on manual applications); in the dash harness there is the same connector that is the neutral start switch on the clutch pedal(abandoned in place on automatic applications) in the harness. The BCM is programed as to which to use. I do not like BCM but I know if it's in there we must keep it "happy"! When a BCM is "not happy" it takes hostages, I.E.: refuses to turn stuff/lights on or off, or even close the windows or turn on the radio amplifier.
(CAUTION: RANT: BCM is not a friend of mine. I think the BCM in my RV has a red stapler. RE: Office Space)