A lot of tuners will just send you an updated file if you add something new like headers or an intake.
Yeah, if you can get an updated file without paying for it then that is a different ballgame.
Does the tune void warrenty?
Different dealers seem to have different stances on this. Some don't mind while others are willing to blame the leak in your moonroof on your new tune.
My advice would be to talk to the service manager away from his superiors and try to feel him out a bit. I did that at my dealership and they were really cool about it. They told me that they wouldn't void warranty on anything they couldn't prove was a result of the aftermarket mod, but I know not all dealers/service managers are straight-shooters like him. (I'm aware that's not a legally binding agreement or anything, but the owner of the dealership is a family friend who would be quick to help me out if there was a problem, so that answer was good enough for me)
The other thing about a tune is that you can "unload" the tune and go back to stock pretty easily. I'm not sure if the unloaded tune could be traceable in the trucks computer, but I betcha Pirate Air, SOCOMech, or one of the other Ford Technicians here could answer that question....