I see why it's confusing, and perhaps we should change the naming here.
Regarding alpha channels: Alpha elements are separate because some of Terragen's elements need "chromatic alpha" which can't be represented by a single alpha channel. I wish chromatic alpha was more widely recognized so that file formats and applications would support them natively, but I seem to be the only one talking about it.
https://planetside.co.uk/forums/index.php?msg=239993Your clouds won't need chromatic alpha (unless you use coloured density inputs), but the alpha may still come out tinted slightly yellow. If so, this is caused by the atmosphere. Any amount of atmosphere between the camera and the cloud could tint the cloud RGB yellow, and it also tints the alpha yellow because (1) Terragen's elements are designed to be composited using an additive workflow, and this applies to the alpha channels too because objects and volumes mutually holdout each other, (2) atmosphere alpha is chromatic, so when it acts as holdout to the cloud alpha it doesn't just darken it, it tints it yellow.
You can avoid all this by making the atmosphere invisible (or turn off "enable primary"), then your cloud alpha will be grayscale. But in order to maintain this generality, alphas are separate images.