And it could be the result of lichens.
But you are not really serious, right?
The blocks I posted an enlarged pic of (from the same wall) don't show any mortar.
And the 'gaps' are shadows. I can post a similar image using YOUR photos.
And your arrows point at NOTHING at all.
You can see that the shadow on the Sacsayhuaman block is not shadow because the sun is obviously casting. I'm not convinced that it is shadow on your picture though It looks like gaps to me.
Look carefully where I pointed to the mortar. It's exactly where I expected it to be holding in the smaller pieces that are more difficult to fit precisely. In other words they cheated.