If you mean Extended Service Plan (I got one for 7yr/70K)......Factory maintenance service should have nothing to do with warranty. Of course Ford won't put a new conical filter in your CAI... but they should do all the scheduled maintenance.... or so my dealer says.
If you mean extended warranty then DJ and mjh hit the nail on the head...
although with a good dealer relationship the small stuff should be fine and things like the electronics, etc. that don't relate to the tune should be easy, but not guaranteed. Technically, according to a ford TSB on 2011, a CAI is potential grounds to void an engine/powertrain warranty.