I asked htc the same question and here's their reply...
"Thank you for your reply.
Gary, the holes on the back cover of your phone are for the microphones that are used when you are takeing videos. The hole closest to the camara lense if for voice and the other is for background noise. The two microphones together are used for noise cancelation.
It is possible that the back cover that you are using with your extended battery may not have been specifically designed to be used on your HTC Thunderbolt which could be why it's makeing noise.
Gary, I believe we could provide the information you need faster and more efficiently via telephone. You can call our Technical Support department at 1-866-449-8358 from 6 AM to 1 AM EST. Of course, if you’d rather continue via email I am more than happy to provide whatever assistance I can."
But when I called htc they told me the dimples / holes are there from when they made the cover thats just how the cover turned out and that they are there because in some way they hold the antenna portion of the cover in place. So according to that CSR at htc that i spoke to the holes do nothing and the reason they are missing from the extended cover is because the extended cover is not made by htc it's actualy made by someone contracted to make it to their specs for verizon and since the extended cover is slightly different in its antenna layout the holes / dimples werent needed.
my first thought was that it was for a rear mic, except that a known issue is that when you record, it uses the bottom/front mic, which is why the audio is so soft (poor) when you record video. at least we know a fix is possible if there's actually a mic back there.
If you pull the back, it is easy enough to see why the holes are there.
There are no mics behind the two holes. The holes are where they attached the metal contacts on the inside of the cover. It's funny that alot of cases have a cut out for the two holes.
At least that's what it looks like to me.