I'm not chemist by any means but here are some thoughts: What did the shop say about cure time for the repaint? Is the work covered by a warranty? Optimum Car Wax is water based but once it dries/cures, it is no longer water-soluble, otherwise, it would wash right off. A product being water based does not neccessarily indicate that it "breathes". The whole point of paint protection is to seal it from the elements. Perhaps the paint will still cure with OCW applied but to be safe, and avoid violating any warranty issues, your paint should be just fine withought protection during the time the body shop recommends for paint cure time.
Did a body shop or a Ford dealer do the paint work? I would think Ford would only make recommendations regarding factory applied paint since it is catalyzed and cures due to a chemical reaction and it cures before it leaves the factory. I would ask the shop that applied the paint what their recommendation is regarding application of sealants/waxes on their paint, just to be safe, since they know if they used a catalyzed paint or a laquer paint which does need time to outgas..