The thing is that in the VAST majority of warranty claims, there is no reason for the dealership to suspect or investigate whether the car was tuned or not. A tech is not likely to waste his/her time trying to determine whether a tune exists. Granted if the car is towed to the dealership with a rod hanging out of the block and the car has obvious bolt on mods, they might be suspicious. However, that or other catastrophic failure is very unlikely if you use a good tuner.
I have had tunes on my last 3 vehicles and never had an issue with warranty. My MKS had brake work done under warranty after being tuned. The Continental had a power seat module replaced. My Mustang had the instrument cluster replaced. About the only thing you have to FEAR about warranties being denied is FEAR ITSELF.