It won't void your warranty. However, dealer servicing your car may give you some goodwill if your car has a major problem just outside of the warranty period. Also, some may see a dealer stamp as giving greater resale value than an independent. At the end of the day, it is your choice whether the additional cost is worth the two factors above.
But, whatever you do, do not take it to Ultratune / Kmart! Take it to a VW / Audi specialist instead if you go down the independent path.
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