This really depends on what dealership you go to and what their ideas or on voiding warranty. Some dealerships are mod friendly and will install mods and not void warranty even if you did the work yourself but others are very strict on any mod.
If you are told they will do the install and warranty will not be voided, then they will back it. They are likely only giving warranty on the labor anyhow, they will not be giving you a warranty on the aftermarket parts. And it means that they are probably not the type of people to report your vehicle as they are instructed to do per vwoa.<This I know is true, and I know if they tell you what I wrote above, they are pretty much saying that they don't agree with the vwoa "mod turn in policy". I know this because all of my mods were done by my favorite vw shop...^-^
Just ask them if they are mod friendly, if they don't know what you mean then they probably arn't. My dealer wasn't really mod friendly and I was stage 2 with a downpipe (catted) for along time, they "reported" my downpipe (atleast it was noted on my paper work "vehicle has aftermarket exhaust (with cat)" but it never caused me any problems, now if it was catless it probably would have said "without cat, no CEL codes" meaning I'm chiped or something. This is specifically why I put a cat on the DP I built.
just because a dealership installs aftermarket parts for you does not mean they wont void your warranty.
They cannot void your warranty because of aftermarket parts, they have to be able to prove the aftermarket part caused the failure if the vw part.
i would still ask how they feel about aftermarket parts, its not worth getting hassled over everytime you take your car in. O0