Actually, having it professionaly painted was not a factor in my decision. It was the same problem you just cited. On my RV-6, there were a number of flying characteristics I wanted to address but didn't because I didn't want to try and touch up Polyurethane paint. It was hard enough to get it on the first time, I just chickened out from touching things up or trying partial repaints, etc.
When I did the Rocket, I had some of the same adjustments to make. Without a second thought, I moved the position of the vertical stabilizer, added a rudder tab, cut up the empennage fairing, changed the wheel pants, added some stuff to the cowl, etc. Then when I had it painted (which I could have done myself), I knew that the airplane flew straight and true.
In the end, I don't think it's that big of a deal which way you go. Both approaches have pros and cons. These are just mine which affected my decision. To each their own.