I noticed the same bolt when I had my primary cover powder coated. I assume it is to help support the cover or to help keep the cover from crushing in the event of dropping the bike on that side.

 

If you look at your old cover you'll notice that where that bolt goes through the casting has a long tube cast in the cover. On the older softail 03 to 06 (I think) that bolt goes on the right of the inspection cover. When I changed mine it required a small rubber O gasket. My guess is that they still needed to support the middle to cut down on vibration and to make the outer primary cover more solid. JMO.