I found out recently what the difference was between alpha channel and premultiplied alpha. If I remember correctly (I think Mark Bremmer enlightened this somewhere), the alpha channel is a mask for the objects based on the geometry. The premultiplied alpha also takes the transparancy in the mix. So if you have shader based transparancy (with alpha masks or 'transparancy' in the shader tree), you should render with the last option.

I am not sure about what clouds would need though.

Hope this helps!

Hoof