Bottom line...Yes. ANY mods during the warranty period MAY (depending upon how cool your dealer is) be grounds for voiding warranty. Sez so in it. If they wanna be a D... about it, they can blame any issue on the aftermarket added part to cover for failures. My '11 developed a clear case of chain slap in the T-case and the selling dealer threatened me with telling the mothership that it had a programmer and that stressed the transfer case-even though their commercials show trucks hauling giant machinery out of bottomless mud pits, and all I pulled was a car trailer.
My recommendations to Customers are if you want to put a programmer in a vehicle, there are 2 types of programmers: one that piggybacks into wiring harness and just modifies the signal going to injectors, etc. (Currently running Edge w/ Juice module in a '17) and the kind that flashes the ECM with new maps (the programs that the ECU runs the components with) like a Bully Dog, etc. Had high pressure fuel pressure sensor failure on '17, brought it to local CDJ (not R, sigh) cool dealer for warranty repair and the trick is when they go into ECU to reflash, if you have a programmer that changes tunes in the ECU, that can be seen and yr busted. Something that modifies the signal can be unplugged and the ECU (and dealer) is none the wiser.
Oh, and you can stomp way more HP/TQ on a standard output w/ programmer/cold air than HO for less, if speed and not absolute pulling power