I have learned early on if something is cosmetically unsatisfactory but structurally sound, LEAVE IT ALONE!! I had a very light smiley on one of the hinge bracket rivets so I decided I'd replace it. After I got the rivet out a portion of the manufactored head was stuck to the paint/powder coat of the hinge bracket. I used a sharp wood chisel to unembed the rivet head and in the process successfully managed to gouge the surface of the bracket. I polished it it out and contacted Van's and they said it would be fine.
Here the internal structure of the vertical stabilizer is all put together.
I wasn't very happy with the first flush rivet on the VS skin. I had tape over the rivet set so I wouldn't mar the skin. The result left a slightly "domed" rivet head. Although it was hardly noticeable and one rivet out of many on the skin, I decided to leave it alone since it was in a bad spot. I will take the tape off of all the flush rivet sets from now on.