I have been looking at edges under a light microscope myself quite often. I found that the the amount of light and varying the angle between the light source and the blade can make things look very different.
If you look really well at the pictures in the OP that are used to prove the difference stropping can make you will see that the lighting is different. Just look at the part of the blade beyond the bevel. This may make the differences before and after look larger than they are in reality.
Looking at the pictures of scienceofsharp it makes me wonder whether the effects of stropping are very significant. Even at such magnifications the differences before and after are very modest. The burnishing effect of linen stropping is most significant IMHO.