I asked my dealer the same question before having my audio system upgraded. I was told that if a fault arises and it is linked with something that has been changed from standard then the warranty won't apply for that particular fault. Anything else that happens that isn't related would still be covered under warranty. I guess you have to ask yourself whether you trust your dealer to be honest about any faults which may arise - not sure how far they would go to try and get out of paying to fix something
