Tuners change the "Tune" of the truck, So they can affect the engine and hence be the cause of a failure. Ford and most dealers will look closely for signs that "Tuning" the engine caused the failure.
There are different signs that signal that a tuner was used. The PCM and others onboard computers can save data that may indicate that you were over Turbo Boost, Running the injectors hotter than factory settings. Burn patterns on the pistons can indicate that fuel was delivered in a different ranges than factory settings. So you may pull a tuner out of the truck before you take it in for repair and the dealer can still spot that a tuner was in use.
Thats said. Installing a tuner is not automatic warranty denial. But if the signs are there that you pushed or abused the engine, Then warranty will probably not be available. And rightly so., If you want the engine to do more than what Ford designed it to do, Then you should be responsible for the repairs.
I had an Edge Evolution on my 2006 F350. My service advisor and I often discussed the feed back I got and used that data to help diagnos any problems I had. The Edge would display engine codes and I could call and ask my advisor what code xxxx referred to. I could even clear codes. Which on one occasion allowed me to start a dead engine and drive into the dealer for repairs. They never worried about that product in that truck, But then I never had any problems that were common to tuned trucks. ( I used it more as a monitor than to tune, Keeping the truck at it stock tune). If I had stretched head studs or burned a hole in a piston, I'm sure the tuner would have come into question. But the problems I had such as replacing glow plugs, wornout FCIM or HPOP were common problems for ALL trucks and not tied to the use of a tuner.