If you have an issue that could be related to your mod, then remedial work at no charge could be refused. You won't get a blanket invalidation of your warranty e.g. dodgy headlight won't be refused because you got an aftermarket exhaust.
Get lowering springs and you've kissed goodbye to any suspension related warranty work. That's why the tuning boxes are so popular vs remaps. Easy to remove if something happens to any of the drivetrain, which may or may not have been caused by the tuning box. I've had a turbo fail on a non-modified Polo at 4k miles in. If something happens to the drivetrain on my GTD, I wouldn't feel dishonest removing the box because chances are it would've gone anyway.
A new set of wheels in 18/19" shouldn't invalidate anything because they can't really adversely effect any other component they're attached to and VW fit those sizes as original euipment. Could they refuse suspension issues with some ultra hard ride 20"ers? Possibly, if VW don't have an equivalent size available for your model.
At the end of the day, warranty work is the dealership's bread and butter beyond selling cars. Their biggest fear is doing work that VW won't pay for. If they know something about your car that could invalidate the warranty but there's no way VW could find out about it, then chances are, they'll do the work and take VW's money.
