That's why APR has their APR Plus program, where you are paying extra for a third party warranty APR administers.
Of course, you if intend to modify the car past the APR Plus program, you may end up voiding that 3rd party warranty.
But, the old saying goes: when you mod, you are your own warranty
Yep.. Going through this "dilemma" right now with my new R. I've never really cared much about car warranties--until I had a new car with a 6 year warranty on it. I had APR stage 1 on the Alltrack, and really liked it. I was planning to go IS20 on it, but bought an R instead...
I didn't go "Plus" on the Alltrack, since I figured I might be adding more power. With the R though, I don't know what I'd do with more power than the Plus tune on public roads. Tempted to go APR Plus, add an APR intercooler, and call it a day.
I did take my tuned GTI to a local dealer for a warranty repair (leaking water pump), and they did not flag the vehicle as tuned. Seems like this is just luck of the draw, though.