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When the fenders are installed they will pull the sides flat...assuming the fenders are true. The fenders cover a good portion of the bed sides so it's questionable just how much of that low spot will even be visible.
Like Charlie said, you'll need to bolt the fenders on and see how wavy they really are. If you pack the outside with bondo to fill that, you'll create two new problems. One, the inside will have the same wave and warble that you're trying to hide here, and it will show a lot more since you can see the whole inside, not just a little bit around the fender. And two, the heat from the filler will distort the panel even more, and you'll really struggle with doing anything with it.
