Send over a screenshot if you ever get weird skies again. Your description is good and I appreciate it but I just cannot see it
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The mod only changes the 'High Clouds' texture of a map, a seamless pattern image that gets repeated over and over by the engine. Enable the Quadrants.tga texture (Random Skies/Textures/Custom/Quadrants.tga), select 'Custom' in the Launcher and see for yourself. Middle (or low) clouds remain untouched by the mod.
When flying at (really) high altitudes you will notice the sky begins to distort in the horizon. It is not that noticeable with 'clear' textures though. Keep this in mind when flying Jets or strategic bombers and select 'Light' skies for missions at high altitude, if you care
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Speaking of light textures, I normally leave it at random but I got a little tired of repeated cloudy skies and I found a source with an additional 23 light textures and there are less chances of cloudy skies now. It will all be released in the next version, sometime after 4.14 comes out. All textures will be also included in the main download and the texture-pack will not be required anymore.
Cheers!