I had this same issue. If you create a couple of files in the BoulderCo folder it will remove the error message. I created a Terrain folder and added a file 'terrain.cfg' with just a single line
EVE_TERRAIN{}
In the Atmosphere folder I created 'atmosphere.cfg' with the line
EVE_ATMOSPHERE{}
This cleared the error, but it doesn't set up any config. I tried going with a default config for atmosphere which was not pretty. There are quite a few values for both tabs. When I have some time to play with it I'll see what it can do.