This is probably because the atmosphere alpha subtracts from the surface alpha. It seems strange that it does this, but there is a good reason. It maintain a purely additive workflow where surface + atmosphere + cloud adds up to 1, and it does this for alpha as well as RGB for consistency. The surface alpha represents the contribution that the surface has to the final pixel, which is diminished when it's partially hidden by atmosphere. This makes compositing simpler in some ways, but more difficult in others.
It used to work differently but it made it harder to composite atmosphere over the terrain, so we switched to this purely additive workflow. But it has this unwanted side effect of making it harder to get a separate matte of the terrain.