I've had this conversation with the service manager at my work before. He said for an example if you change the wheels and your gearbox fails the could reject it because its got non standard wheels which means it couldve put more pressure on the gearbox causing it to fail.
The last thing he told me was that its also upto the dealerships descretion. If the service manager is alright then he might still do the warranty for you. After all dealerships do make money from doing warranty jobs