installing torque boxes to a finished car

You wouldn't need to have the rockers repainted. Just mask everything off to protect it and be careful.

If you do damage the finish on the pinch weld, it can be repaired with a detail gun, then burn in the clear.

The repair area would be very small and it would be low and under the car, out of direct sun.

You never want to burn in clear on the upper body because it will fail, but in the area you are talking about, it would be fine.