After market remote start or security won't automatically void your warranty. If, by chance, the installer does a terrible job and somehow fries some electronics/wiring, in that case the warranty claim would most likely be denied and you and/or the installing shop would be on the hook for any and all charges for the repair. Find a reputable shop that sells either DEI (Viper, Clifford, Python, Avital) or Compustar (my favorite by far) and you'll be OK.
FWIW, my 2008 4Runner has an old Avital alarm/remote start that I installed 10 years ago, no issues ever. My 2014 4Runner has a full Compustar alarm/remote start/Drone mobile (highly recommend this) with no issues as well.
It's very rare for one of these alarm/remote start systems to go out or even damage the electronics of a vehicle. It's far more common to have a half-assed install that causes all sorts of issues with both the vehicle and alarm/remote start system. As long as you go with a good installer, you shouldn't have any issues.