The 3rd brake light is subject to a lot of water - everything that runs rearward from the roof. As someone mentions, the stock setup is notorious for leaking. When my truck was a few months old my light went out due to water filling up inside the lens and shorting out the bulb. I fixed it literally in minutes in the Home Depot parking lot with some rubber weather-stripping around the top and sides (left the bottom w/o to allow water to escape, if necessary). That was 6 years ago and all has been fine.
I'm not sure if your situation is the same but I personally would be hesitant to goop it up with silicone since if/when you have to take it apart you'll be fighting whatever "goop" you put on there. A (better) rubber gasket than what comes with the light is probably the best way to go. Not that the silicone won't work.
