That a curious problem. I have yet to use MCW paints, so can't comment specifically on them. But I have chimed in here just to say that I seldom use a clearcoat unless the specific job requires it for one reason or another, and have not incurred this problem. This is true whether I paint with acrylic, lacquer, or enamel. I cut the paint with 3600, 4000, or 6000 Micro Mesh pads, depending on how good the paint is to begin with, then polish with finer Micro Mesh pads, Tamiya polishing compounds (usually just Fine and Finish), and finish off with Tamiya wax. I wonder if the problem is specific to MCW enamels.
Repainting after waxing could be tricky. It may depend on what type of wax was used. Tamiya wax seems pretty forgiving. I have not tried to paint over a waxed surface, but I have glued to it with no problems. With enamel paint you may be able to wipe the body down with alcohol (but don't try that with lacquer or acrylic) though can't say for sure it will be effective at removing the wax. It may be difficult to ensure all traces of wax have been removed, even with a good wax remover. It may be worth painting a spoon and giving it the same treatment as the car body including wax, then try to remove the wax and repaint.
Just spit ballin' here.