Yeah, Matt told me that the planet wasn't "captured" by the Planet test group, so it wasn't part of the group even though it was inside the group's area (ie. bright white line box drawn around the node in the Network View), easily fixed by either dragging the node out of the group and back in again, or by right-clicking on the title bar of the group and selecting "Group: Capture Nodes". And the new planet should only have the cloud connected to it, not atmo, or anything else. Also I needed to un-check "render surface". For GI he recommends rendering a GI cache on the scene that includes both planets (i.e. no need for a render layer), and use the same cache for all layers so that lighting-wise they all fit into the same environment.
Further, he said that for the cloud render layer, under "All other objects" to set Render to Holdout and enable Cast shadows and other rays. When rendering the layer with everything some settings are reversed. You'd plug the "cloud" planet group into Object Group 1 as before, but set that to Render Invisible. For "All other objects" you want to Render Visible and enable Cast shadows and other rays.
What I'm trying to figure out now is probably simple but now sure which file format/setup will give me an alpha like what a png does.