A lot of it is going to depend on your dealer as a whole, and members of staff who you, or even just your car, come into contact with.
If your dealer sells you a VWR kit they will warrant the kit and the car and bend over backwards to make sure any problems are sorted in a hassle free manner. If you take that car to another dealer in the same retail group you'd expect the same service.
However if you're away on holiday and your car plays up, you may well find the local dealer not so helpful and more reluctant to claim on stuff that's not factory approved until you really pressurise them to pick up the phone and speak to the dealer who sold you the upgrade. I've found in most cases the bigger dealers are the worse ones to deal with. Most but not all.
Other upgrades, be they LED rears, different stereos etc will also come down to the discretion of the dealer. If you've invaded the vehicles electronics with 3rd party software (VCDS for example) then you're inviting VW to show you the door or ask to see the colour of your money when making a claim on a modified vehicle, especially if it is an electrical or sensor fault.
They probably look upon it as ''well, he's messed about with the rear lights and the radio, so what else has he been meddling with?''
Company cars and anything with a lease and you're out on your own. The paperwork will normally stipulate that you don't modify anything on the vehicle, your insurance will too.
It is the same with your computer at home, your smart phone, even your vacuum cleaner, if it is under warranty and you wish to modify it, you're running a risk. If you want to do it you probably will anyway so are fully prepared (no matter how reluctantly) for the potential consequences. Que sera.
