IMO- Deal with it now or spend more time and money later. Sand it down, remove the body sealant they use in the factory. Coat it in POR 15 and then pain it. This usually happens when the drain holes are clogged. You might want ot look into making them better or bigger.
Ok here is a picture of the tailgate after I sandblasted then did the POR-15 thing to whole [part.
Notice how I bent the seam up. First I had to grind the spot weld then use a chisel to start the bend up. Then I was able to use a large screwdriver(or pry bar) to bent the rest up.
After than I took some big pliers and squeezed it flat and nice. Well sort of. After I painted the POR-15 on both sides and inside the gate under the inner skin I pounded the seam back down with a ballpeen hammer and then worked it flat.
Unfortunately I did get some ripples in the outer skin. So I had to use a slight amount of filler over it to get a smooth appearance. But it was only a little.