That being said I took my car to Royal for my 10k service and not a single word was said to me about my mods... And theres no way they're missed that big metal APR Stage 3 turbo inlet. Obviously if I sling a rod out of the side of the block they're probably going to tell me to GTFO -then again I know they've warrantied at least one Stage 3 MKV GTI that popped a motor but that tech no longer works there - but im pretty sure if something like my waterpump were to fail they'd take care of it.
If you're worried about doing a tune and bolt ons just swing by Royal and talk to Terrence in the service department. I will pretty much only deal with him and he even specifically asked me when I brought my car in for the 10k if it was chipped or not so he could tell the tech not to flash my ECU. Let him know of your concerns and he'll probably set you straight about what they can or cant do.