The thing is, whether there is a footprint is relative to the parties doing the looking & the methods they employ.
If you bring your truck in for warranty work on, say, a window regulator, there isn't some red flag that pops out of the tailpipe outing you to the dealer.
But, if your engine explodes you might get a dealer who is able to get the warranty work covered by Ford with little fanfare, and isn't looking for ways to deny you, so they don't go looking.
In other cases maybe a dealer loathes warranty work and looks for any reason to deny it. In this case, it depends on what tools they have at their disposal, and what evidence they can peice together to say you have a tune. For example, they might point to time since last DTCs cleared as evidence, while you say you just replaced the battery, etc. Its a he said/she said, but I don't believe most dealers can concretely prove a past tune.
But from what I've heard, its only when Ford corporate gets involved, with engineers hands-on with either your data and/or your engine that they have the resources to determine if truly your engine has been tuned. If that happens, I think you are in trouble no matter the tuner - maybe even the "spoofing" tuners like JB4 can't evade such detection.
But the chances of that level of scrutiny are pretty low, I would think; you'd have to blow things up in a pretty novel way for the dealer to call in the Corporate Cavalry.
