That's bullshit. It has to be proven the mods caused a failure. My local dealer put a whole new engine in my scion. When it got to them, it had a painted valve cover, header, intake, all sorts of stuff. Didn't even slow them down. They warrantied it.
Maybe they thought it was the wheels, so they were like no, not gonna check the wheels?
Still, BS. Magnusson moss act or whatever is the law suit that makes it so they have to prove the mods caused a problem. This was big on Mazda forums, as Mazda was flagging all sorts of cars.