If you get it actually powder coated the filler will need to be a conductive metal such as solder. Any regular autobody fillers or similar won't respond the the electric charging and make the powder stick to the frame. If it's a small dent or two that are quite shallow the amount of weight you'll add is negligable. You'll need to totally sand out the area and then use plumber's solder and flux along with a propane torch. Build the area up higher than you need and then file and sand away the excess to blend the dents.

If you want to just use Bondo or similar then you would have to switch the plan from powder coating to regular painting.

Or perhaps given that powder coating is becoming so mainstream they may have a metal particle style of filler that is conductive. Try asking the coater.