Mine uses the same key for everything, I took delivery dec. 1. I was pleasantly surprised by this as many people had mentioned their 07s had separate keys.
Must be a Job 3 thing, my truck is a Job 2 vehicle and the keys are different.
Dale, try taking your truck to a different locksmith. There is at least one member that has had the tonneau cover rekeyed to work with the ignition key and I will be doing the same very soon.