Tbone, I have heard the same thing about the radio touching the riser clamps being bad for the radio. I dont know anything with reguard to swaping to thiner clamp bolts.
What i do have to offer is an alturnative method of obtaining additional clearance. During a yaffe Monkey bar install i did recently, i ended up having to shorten the handlebar riser by 3/8's of an inch. its a long story why, but it had to do with the sweap of the bars and the fairing openings.
Anyway, the result was also nearly 3/8's of an inch gap between the radio and raiser clamp. It cost me like 15 bucks to have the local machine shop place the uncaped riser upside down on the flat plain of an upright mill, and shave off some materal. removing one clamp and riser at a time is a relitivly simple matter. And you can remove as little materal as you might wish, just as long as its equal from both risers.
Not saying its the best solution, just an alturnative, should nothing else simpler work out for you.