I would like to animate parts independently, and maintain a buffer between the objects. By buffer, I'm referring to the gap between the cloud and the sun. For example, say the sun rotates in a circle, and the cloud is displaced by a map. I'd like to keep hard edges on the objects. The "gap" would show the transparent background. I've tried different combinations of track mattes, masks, and choker mattes. However, I know there's got to be a better technique that I'm missing.
I'm thinking that a white Stroke on the cloud which is supposed to be in the front would do the trick. Oh, but you want what's the white stroke in the sample to be transparent, correct? How about putting a blue stroke on the foreground cloud, then doing a simple Color Key to remove the stroke? That should give you your "buffer". Then output your animated file as a Quicktime Animation, millions of colors+, which will give you an alpha channel. Or a PNG file sequence would do the same, depending on what your deliverables require.