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Clouds are all the same color. The darkness we see is the shadows from other clouds.

No, darkness comes from density. The denser the cloud (the more water it contains), the less light can come through, thus it looks darker.

Even very dense rain clouds look perfectly white from above. They all reflect light back into space.

How come you sometimes see very dark, lonely clouds in blue skies?

Likely because they are tall and tilted in a direction facing the sun, so that the moisture blocks more of the light than it would if the sun was hitting it at a more oblique angle.

Your relative position to the sun and the cloud.

I am not convinced. This would mean it could only be "blocking" the sun. If anything, it would be atmospheric light reflections blocked. In any case, it's not "other clouds".

I think diffraction has to play a role. Why wouldn't it? Dense, or raining clouds certainly have different water droplet sizes and shapes than fine, fluffy clouds. They may even reflect the ground or sky at some point, I imagine, like the ocean.

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