I do not know how this is covered by the warrany agreement, other that the standard statement about unauthorized parts, or repairs invalidating the coverage.
This is my take on it as to what will likely happen with 2 scenarios:
If you picked up 12 volts from the line going to the rear accessory outlet, and then you had an electrical fire in the engine compartment, it would be stretch for them to say your tapping into that wire in back caused the short.
If the stock radio or CD player dies and you are tapping into various inputs and outputs of the audio system, I think you will be up against the wall, even if you know the failure has nothing to do with your mods. It doesn't matter because you will not be able to prove that you did not damage something in the process of making your modifications, even if the mods themselves have no relation to the problem.