I had an '87 Camry have a similar issue & little later later in its life (about 9 years). It was not caused by stone damage but found cause was an improperly installed windscreen. rust started behind the mouldings on an edge seam & festered working outward to where it was visible. Eventually rust hole formed under the molulding allowing water to leak into the cabin.
Hyundai likely will argue that it is not perforated through, as that's the actual rust warranty. Saturn would not cover me on my VUE rear lift gate handle for similar rust. Rust bubbles formed around the chrome applique handle in less than 2 years. This was a known issue from poor process, yet no claim would be valid unless it perforated.
