The EcoBoost is no different from any other engine in this regard. The existence of modifications is NEVER enough to void a warranty because of Federal law. But any damage caused by the modifications will not be covered. Traditionally gains from tuners on gas engines are modest at best, and as a result it's rare to see an engine blown up from a tune. But these turbocharged DI engines are capable of some pretty serious power gains from a tune, and yes it's possible to break something.

I think when considering stuff like this you should ask yourself. "Am I okay with a $10,000 repair that's not covered under warranty?" If the answer is "no" then you shouldn't tune the truck. An exhaust is highly unlikely to cause issues, but an intake very well could if the air filtration isn't as good as the stock system. That's because dust particles can "dust" your turbo and cause all manner of mayhem.