Well, sure a lot of downloads. I hope it helps people with grass.
I've dived a little further into the problem, and found that within the Population Mask shader the Surface Layer that is masked by the Fake Stones isn't fully masking. In fact it's like there is some opacity on the mask.
Update: I've fixed some noticeable errors after coming back to the project, but still, grass through the rocks persists.
Here is a comparison of the stone mask, and the final mask


It does vary slightly like the Surface Layer is not masking correctly by the Stone Mask.
Any ideas what's going on, or what I'm doing wrong trying to combine a PF mask with a Fake Stone Shader mask?