That problem can only be fixed on a new tailgate or one that hasn't started to rust yet. The problem is the seam where the skin wraps onto the frame of the gate. That creates a nice trap that collects water and any dirt that gets inside the gate. I think I have beaten it by:
1. Enlarging the drain holes
2. Removing all the internal parts, Under coating the inside of the gate, and filling all the seam cracks with undercoat (not seam sealer, that stuff eventually allows water between it and the metal), an I mean fill till there is no visible evidence of a crack between the two surfaces.
I have been successful in saving a tail gate that only had a very minor bit of rust inside before doing it. Once rust gets started there is no stopping it unless it is only surface rust. If it gets beyond surface rust the only way to get rid of it is to cut it out and replace the metal. That could go as far as complete panel replacement.
Good luck,
>-