Talked to the SCT people. If I had the trackey engaged and loaded the sct tuner with that ecu configuration, that would go into the tuner as the stock tune. However if I changed something , say the rev miles, and tried to load that into the ecu as a custom tune, it would error out.
So what I'm seeing, the trackey is only good if you're going to use your boss for the track and street, with no other engine modifications.
If you want to modify your engine, say headers, cold air, supercharger, etc, and want to retune the engine to optimize those mods, the trackey is no longer of any use. A choice you need to make.
I have the trackey but don't take my car to the track, so it's really of no use to me. At some point I plan to out a supercharger on, and at that point I'd use a tuner instead of the trackey to change engine parameters......Although I'm really pondering why I think I need a supercharger, since the tires can't handle the stock engine power now!