Hi DonL. If you mean Ford will refuse a warranty claim for problems resulting from an owner reprogramming their vehicle using FORScan or any other programming software?
The short story answer would be yes. If Ford determines an issue was due to modifications/alterations by a vehicle owner, then yes, it is likely Ford would refuse warranty coverage for problems related to those owner performed changes. They (and any automaker) would certainly be within their rights to do so.
However, keep in mind that denying a warranty claim as discussed above is not the same as a voided warranty. A voided warranty means nothing will ever be covered again under warranty. Even issues unrelated to the reprogramming/modification. In the real world, very few things result in a “voided warranty”. Salvage titles, caught using the vehicle for racing, etc. etc., are a few examples.
Also, according to your most recent descriptions (keyfobs hanging up, no one near them) … it would seem it may not be a case of accidental panic alarm button presses. So reprogramming the system to require two presses would not help anyway. Again, only going off the information provided so far. If this continues, having this diagnosed by your Dealership may be a good course of action.
Hope that makes it a bit clearer, keep us updated and good luck.
EDIT- Also, have you eliminated any possibility it may be the interior motion detector triggering the alarm, as MattMacMan mentioned?