Yeah, after my past experiments I gave a description of how X-Plane used the texture.
Your conclusions are about right, from what I recall. Regarding the sky colors, I think the sun elevation doesn't need to be +/-90 to use the morn/night textures, they're already completely used for a low sun elevation of +/-10 degrees or so, IIRC.
Also, the lowermost 1 or 2 stripes of each 128x32 texture is used for something like fog/haze color, IIRC.
Only a few of the 8 vertical stripes have the effects their name suggest, others control things like:
moon reflection on water;
sun reflection on water;
color inside clouds at the bottom of cloud;
color inside clouds at the top of cloud;
and other various things like reflections, etc.
The 128x128 cloud textures are used for direct and ambient cloud light. IIRC, the X axis represents the sun elevation, the Y axis represents the cloud height. So the colors of a cloud puff depend on its height and on the sun elevation. The color of clouds can be indipendently modulated by a couple datarefs whose name I don't remember ("cloud ambient" and "cloud direct" something).
In general, the final environment lighting is calculated with shaders, and the sky_colors textures are only used as a starting point. That's why modifying the sky_colors textures doesn't allow complete control over final result. Sky_colors textures are basically legacy textures, on which subsequent shaders have been added.
An easy way to check how they work, is making a texture completely black, leaving only a single element (e.g. a stripe) with a primary color and experimenting with the results inside X-Plane (using the provided sky colors console).
Anyway, I think at this point XP12 (hopefully with a totally new lighting system) will come out, before something decent can be obtained by modifying XP11 textures/shaders... 😬