This is a seperate issue to servicing and warranty work. Servicing no issue that I see or have experienced. Warranty work, if necessary reverse mods before it goes in, but only if Mod could be argued to have caused the warranty failure.
If the car is leased or on a HP style finance package, including persnal lease contract, you DO NOT OWN IT, the finance company does, therefore you can't mod it as you are modding someone else car.
Basically same as hiring a car from Hertz for a week and modding that
This is probably why the Seat guy got hammered. If the finance company have to repossses because you stop paying finance in their eyes it will be worth a lot less because it has been modded (will lose big value at auction) and will require remedial work to revert to standard. They will therefore have you if they find out, I suspect that the garage don't care who owns it when they service it, but they could be instructed by a lease company to alert them to mods if would alter the servicing cost, or if the lease company / finance house was VW finance??? But again I think unlikely. So if you own the car Mod away, if you don't, don't be surprised if the people who do own the car find out you have modded it then take you to the cleaners for modding their car.