When air is directed at the center of the cylinder, it will still flow through the fins on the underside, provided there is sufficient pressure differential. The separator plate really just serves to eliminate a circular path of heated air within the cowl (i.e. starting at the mufflers, flowing forward to the front of the engine, aft across the top, down the backside to the mufflers, and recycling forward again...).

This one step, although counterintuitive, is certainly better than nothing.