I would bet somehow the dampening material behind the metal is getting wet and holding moisture. If you never get that out of there, itll just keep going until you need a whole new hatch.
On my 06 4runner, I had a spot beside the license plate that had started bubbling and rusting from the backside. I took it to the body shop to get repaired and they found that the rear hatch lock/keyhole had a seal that was bad and water had gotten into the inside of the hatch. There is dampening material or something in there that holds water and that just was never allowed to dry out because of the closed space. Over time this caused rust from the backside out.
To repair my body shop cut out around the rusted area and patched it back in and repainted the whole hatch, perfectly btw. Total cost was around $650.