Extrude doesn't use mc scale properly
For comparison, the top two glowing cubes arn't using the extrude feature (all the glowing cubes are using mc scale at 0.100)

Shown from the side (right two are using the extrude feature)

As you can see here, the set of cubes experience z-fighting because it isn't having mc scale applied properly (mc scale 0.100 applied)

The mc scale DOES do something however, as you can see the object has z-fighting on all sides without it. (mc scale at 0.000)

It appears the mc scale applies somewhat to the x and z dimensions (completely in the z dimension, only spacing in the x dimension?), but not at all to the y dimension.