Dealers have no say in what is covered under warranty. They try to discourage warrantied repairs because they can't gouge you for the work.
That's one of those old wives' tales. Dealers like to keep the customer happy by doing warranty work because that way they'll get the customer to come back for other stuff.
What dealers don't want is for VW to charge back warranty work because VW determined that the damage was most likely caused by a mod. Some dealers have been burned by approving warranty work, VW determined that the problem was caused by a mod and VW charged back the dealer. Those dealers will often deny claims because they go to great lengths to connect mods to a failure.
Dealers do have the first "say" about what is covered under warranty. If an educated customer disagrees, then they can call VW and argue their case.
That is why it is important for customers to get educated about all of the possible pitfalls of a mod - including those that are nearly impossible - but theoretically possible.
I had a BMW dealer try to tell me once that my driveline warranty was "void" because I had aftermarket wheels. I did, but they had the identical offset, size and weight of the OE wheel and the manufacturer was an OEM and made some BMW wheels. The dealer said "any aftermarket wheels will void your warranty". I asked to use his phone to call BMWUSA and we got that straightened out pretty quickly, but how many other customers would have bought that - hook, line and sinker?