Interesting your dealers view on what is illegal and voiding any warranty recourse.
If you as the owner choose to modify your vehicle in any way than that is your call not VW Australia or the dealership position to play bully boy games.
You could apply the same theory in changing wheels, say your vehicle came with the OEM VW 20" alloys and you choice to fit Audi 21" rims. They still work as designed without affecting your vehicle and your warranty is still valid.
I had a simular experience with my partners Golf, I had enabled via VCDS the TMC to operate on the GPS. After a map upgrade service I quickly checked to see if this was still working, it was not. Questioning the dealer they stated that that was not authorised via VW Australia and they were directed to turn off the TMC. When I explained to them that they had no right to modify the car without our authority as the car was not property of VW Australia they stood down. I then demanded that they return the TMC on, which they did.
As for warranty issues, unless it is proved by the manufacture that your modifications caused the problem then you are still covered.