Unless it rusts completely through, Toyota won't cover it.
The only way to fix this effectively and cheaply is to replace the back hatch door with a high quality used one.
Given that you're in IL and they use a lot of salt during the winter months, I strongly suggest washing the truck, including the door jams, at least once a month. Salty slush sitting in the rear hatch door jam for a long period of time was the likely culprit here....or the rear hatch had been repainted and the repair facility did a poor job and the salty winters took care of the rest.