Frank,
Have you been able to place any populations in the areas where you have the strata shader applied?
It has been my experience that the shader changes the normal shape of the terrain whether it is a height field or a fractal doesn't matter and when you place a population in the area where the strata shader is, it computes the elevations based on the original surface. What this does it to cause the items you have populated to either be buried or floating in mid air.
Has anyone come up with a solution for this problem?