Anything aftermarket is just an excuse to not have to cover the warranty. Always been that way. Lowering it changes the geometry, which is all the excuse they need.
I'm pretty sure Ford will kick it back. Wheels are one thing, but suspension parts are another story. They will just point the finger at you or the installer and say that it's their fault, end of claim. At least in the grand scheme of things it's not a big deal. If I remember correctly the 2015-2017 cars are notorious for the axle nut backing off over time regardless if it's bone stock or a track rat.