I’ve only been using Vue now for the day but the best way I’ve figured out is to do it just like a mask pass in say Mental Ray or Brazil.
Set the background to black with no specular. Turn off all atmospheric effects.
Renders your clouds as 100% self illuminated (aka ambience to the max). Save this out as your alpha.
Render again with a black fog. (Difference of this will be your atmosphere adjust mask)
Set your clouds back to their desired density and what not.
Render again.
Set the first render as your alpha and you have a pre-multiplied cloud layer with an alpha as if you had rendered it straight. And you have a fog pass.