of course they will deny trans/clutch problem from a tune... that would directly impact it and cause more wear and tear. it all depends if they want to do the repair or not, and what they will get from ford for the work
what's a tuned V6 make, 330-340? If its the same MT82, the clutch should have held. Sounds like a factory defect to me. But OP will still need to be courteous and patient when interacting with the dealership service center as they have an excuse to deny a warranty claim.
If the car was in nuetral, no clutch it made a chatter noise, or when you shut the engine off. If you held the clutch in during either of those times, it would not make noise