I bolted on my bungee nuts to a) hide the holes in my rear fender, and b) to help secure items on the rear fender.  I thought the inside bolt heads would clear the oversized tire I replaced with a "fatter" 140-90-15 (140-80-15 is stock).   Apparently this is not a real big deal with a stock set-up.

Well, when I bolted on the bungee nuts, I eyeballed it and figured they would not rub.  I was/am also concerned about my turn signal mounts inside rubbing.  So far, both signals look clean from rubber contact.  The right side has plenty of clearance for my bungee nut inside bolt heads.  Apparently, the rear left clears okay as well.  After my first day of riding with these, I inspected and found that my tire is making contact with the left front inside head bolt (see left hole in photo below, I ended up removing it and scratching my new decal with the fuckin' wrench).  There is some damage to the tire tread as a result (some scratches and chunks-out of the meaty part of the tire).  I'm hoping it's superficial, but am looking into it.

Bottom line, do what you want on the inside of the rear fender, but just make sure you have the clearance so you don't get a tire rub.  I should have removed the shocks to see if contact would be made if they bottomed out.  As for the rubbin' bolt head, I thought about cutting it down but I'm in a "screw-it" mood right now.