The Alpha Channel is a greyscale image that defines transparency, used for compositing different images together in apps such as Photoshop, Shake, After Effects, etc. Basically, a greyscale image mask, just like you would use for an image based blending shader (white is solid, black is transparent, grey is semi-transparent).
If you do a normal render, with surfaces and atmosphere switched on, etc, you'll find the terrain and clouds are solid white, but the sky will graduate from solid white at the horizon to grey at the top. I assume this is because the sky has a depth, it gets thinner with altitude but there is only empty space beyond the sky (therefore nothing to render beyond the sky).
If you switch off atmosphere completely in your render options, you will find the terrain solid white, but the sky will be solid black in the Alpha Channel rendered frame.
If you go to your atmosphere options (where you add clouds, etc) and switch off Enable Primary for the actual atmosphere node itself, then the terrain and clouds will be solid white, but the sky itself will be solid black.
NB: When I say the clouds will be solid white, I mean they will be grey at the edges according to the transparency of the clouds.
Make any sense?
