Sorry to have to be short again, I'm somewhat sick at the moment and not feeling up to solving rendering issues...
Separating the phong shading terms. Either via a single shader and a uniform that says which term needs to be outputed or one shader per term, but they need to be separated.
As I said, the ALS shaders are pretty streamlined, but I have one version which is separable, i.e. contains all atmosphere-rendering information in blocks that you can include independently. I'll make that available to you over the next days (it's not released and also not GPL) so that you can have a clear picture of what the operations are.
Basically ALS computes a lot of geometry to get the light for a pixel (where is the pixel in relation to the sun, the atmosphere and the relevant cloud layers?), so separating ambient and diffuse is not good performance-wise, because you might end up doing the geometry twice. Though at the moment I don't see a smart solution either.