Can't answer your question but here's my take on aftermarket products. There's a little thing called the Magnuson-Moss Warranty Act
Sema.Org and even though there is not a specific provision in MM that says anything about modifying your car there is however several references to using aftermarket/non-OEM parts in the car and it is very clearly stated that they cannot void the warranty if you use aftermarket parts unless it can be shown that those parts directly caused the failure you're seeking to have repaired under warranty.
So here's my point. Whether a programmer leaves a foot print or not if you're pumping the extra fuel into your engine to produce an extra 100 Horsepower – 250 Foot Pounds of Torque I'm pretty sure they'll be able to tell when your tranny goes south, foot print or not. I've owned a lot of new vehicle and I've never had a warranty issue when I took them in for service whether it was with a CAI, Exhaust or lift. But I also research and buy from the best manufacturers that have shown a track record of standing behind their products and I then use the product responsibly.