"Several rear lights set to LED." This prevents the system from initiating a fast flash (or Bulb Burned Out) in the turn signal indicators within the cluster when LED units are installed in incandescent bulb locations in the tail lights.
Oh yes, they can easily see it and revert it if they want to. But most won't bother unless there is something you did that they can prove that caused an issue that you attempting to claim under warranty.
Actually the OEM anti-theft system will disable operation of the starter, fuel injectors and the spark plugs. Even if you "Hot Wired" the starter, fuel pump the injectors and spark plugs will not fire off. Also if you have Connected Services active you can track your vehicle anywhere. Now...