No one can tell you where to get brakes done. Most dealerships dont cover it after 12/12000 except Subaru we are 3/36000 for any adjustments.
However, if you have aftermarket brakes i.e hawk pads, Eradispeed rotors, or Baer calipers or whatever, and have a brake failure or issue, then they can deny that warranty claim if they can prove that aftermarket brakes caused it.
Just having mods wont deny a warranty claim unless the dealership want to be dicks or it is directly the cause.