I'm not sure what you are talking about :O
Toribash's shaders can be applied to atmospheres.
By default there is a built in shader which is loaded. This is just a regular Toribash shader.
The only thing that might may you say that there are different shaders is the fact that "poor shader script" is integrated to atmospheres also.
But it is either regular shader or poor shader, but not both at the same time.
Edit: Maybe you meant modeling was done via moray or some sort of tool like that.
Actually it is only world builder and scripting.
Edit2: Some screenshots of an atmosphere I'm working on
Outer space
http://www.box.net/shared/durn9p7mzb
http://www.box.net/shared/j5gb6comdj
http://www.box.net/shared/e7cyodyhjh
WIP only.