I've noticed that sometimes a bit of sharpening can exaggerate grain, but I have done no tests to establish the exact conditions. The stone micro-texture will be much the same scale as the grain so they will be indistinguishable. As Ian says, smooth areas make it easier to to see any grain that's present.
Or, if you darkened the sky using the Burn tool, it's possible that the grains lies exactly on the boundary between Shadows and Midtones, but this seems unlikely. I had to blow up the image to see any grain. Presumably a bit of Blur would deal with it, if it's visible on a larger print.
I know nothing about Xtol. Might it have had an effect on micro-contrast?
A very satisfactory image anyway.