The inverted engine can have both openings open for looks. You do need to place one baffle plate at the cylinder centerline location, so no air will bypass the engine cooling fins. The cowl cutout can be quite closefitting to the cylinder if the head sticks out. Behind that baffle, you need air extraction with a rim at the foremost opening edge to prevent air entry there. (example Big-bird). That way, the muffler receives it's share of cooling as well.