Since you're buying a Chevy from a Ford dealer, I would say that the warranty would have to be of the type that could be used anywhere. I would darn well never set foot in this dealership to let them work on the truck if you ever needed to use the warranty. I still tend to think that you would be better off getting out from under this truck in the long run. It might seem like a great deal, and I realize that you're getting a warranty but it sounds like you also might be buying a headache. Besides, I'd sure hope that you are expecting the truck to be reliable for more than the 3 year warranty, especially with the amount that you plan to use it. This truck sounds like the kind that might start needing expensive things replaced right after the warranty is up and with the newer common rail diesels you will be appaled at the price of repairs for some common items.
I'll also add some anecdotal evidence that I've amassed since buying my F250. I love my truck, it's been great and although the 6.4 Powerstroke is no fuel miser I also don't drive it enough for that to really matter, and it just pulls like a freight train. As the proud owner of my F250 I also occasionally frequent the Ford Truck Enthusiasts website and read about other people's experiences. From what I've gathered, again anecdotally, the guys who have consistent problems with their trucks, be it the dreaded 6.0 Powerstroke EGR and head related issues or the problem with many of the earlier 6.4 radiators and intercoolers or even the finicky fuel system on the 6.4 seem to never be able to get things 100%. I've read about a lot of guys who have had entire 6.0 engines replaced only to still have problems, or guys who've had more than one fuel system replaced on their 6.4 only to continue to have problems. It just seems like with the newer diesels, once a truck becomes a problem child, it seems to remain a problem child until the owner gets fed up and finds a new owner, then the new owner gets it, and the cycle repeats. I would just suggest to tread very lightly in the hopes that you don't end up with a money pit.