Coming from a dealer's perspective (former service advisor, ask me anything) there are two schools of thought. Some dealers refuse to warranty anything if they see even one modification to a car, because they're idiots. One service manager I worked with refused to approve a warranty replacement for a catalytic converter, based on the fact that the car had a cat-back exhaust. This mentality is basically the old way of doing business, with a little "try and F the customer out every possible cent" thrown in for good measure.
Doubt he's still around and doubt I'll ever have to worry about doing business with him as well, what a prick
The other approach is usually found at dealers that are also selling performance parts; they'll make you aware that modifying your car may affect your warranty, and will still perform warranty repairs for unrelated items, but if something they sold you (or even installed) caused a failure that they can't cover, well, you knew the risks going in. Naturally I preferred the second approach. It would be nice if VW struck some sort of arrangement with APR like BMW has with Dinan, where practically every dealer sells Dinan parts and there's never any conflicts when it comes to warranty repairs. Or, they should do it the way Ford Motorsports does, and offer warranty-backed parts and tunes through their dealer network. In both of those cases, they're selling a car that they know people are going to want to enhance, so why not give them an option that's A) has less uncertainty and B) brings in some additional profit?