Now we know... The big secret is out. It's an antenna.HTC was interviewed about the components of the design and they exposed 2 key components.
One is the vibration motor which you can see after you take off the battery cover.
Second is that gray dot, its actually the antenna.
The reason for this is because the design of the ThunderBolt is a unibody aluminum design much like the Desire HD and HTC Legend. also if you look at the first accessories that were leaked that confirmed the model number of the ThunderBolt being ADR6400 you will see that the "dot" is cut around like the kickstand is
At least its not on the sides of the phone where you will clearly kill the signal.