I believe that @jthornton is recommending that set-up because hens like to sleep on the highest available surface. (correct me if I'm wrong) So long as the roosts are positioned high enough that the hens aren't tempted to sleep (and poop) in there, I would think the current setup would be fine.Do you find that having an additional next box accessible directly from the run is helpful?
If you're thinking about any major modifications, I'd be more interested in being able to get into the henhouse itself, especially for cleaning and possibly for catching the chickens. (Mine's designed like a shed, and I like it that way.) There are few things less dignified than having your bum poking out the back while you twist around and try to reach that one stubborn pullet... In short, I'd enlarge the door. Or make the whole wall away from the run into a door. But that seems like a very involved project.