Same here, I've been very hesitant to do this. From everything I've read, Ford is extremely picky about aftermarket addons let alone tunes. There is literally a service guide written by ford telling techs how to look for mods and tunes, and what issues they can say are caused by said mods, even if they have nothing to do with it.
Many of my previous vehicles were Acura's (that I raced and put turbo's on), and Jeep's (the 5.2L and 5.7L Hemis). Never once had an issue with tunes and warranty services, including extended warranties on any of them. Actually, I take that back, the terrible AutoNation I went to one time with my most recent Jeep tried to blame a tune, but I took it to another dealer and they laughed at that diagnosis.
This thing has me very nervous, knowing that it actually counts modifications and records them as non-volatile changes (meaning they are never erased).