Hold on, you called it a fighter twice in a row. It is definitely a transport, isn't it?
To be honest, it does have more of an interceptor type vibe to it than a freighter, but then if it's atmospheric then it can hardly be bulky and box shaped as they often are in scifi.
What to do with the top... well you could add some stuff like running lights, signage and flaps on the wings just to give it a slightly real world feel.