I'd say...not so sure about that. Right in my Ford Mustang Owner's manual...This is obvious and should be clear to anybody who's considering that kind of modification. It is not what think of when it goes 'REALLY SOUTH'. But different people might think differently about it.
As far as I know there's no warranty issues that do not directly relate to the exhaust system. If the active valves start rattling I of course won't ask Ford to cover the repair cost. If the engine explodes I'm sure Ford won't cease warranty because of an H-Pipe. That's actually more likely if an oil catch can is installed.