You're right, it's not there, and it is a shame, as it's quite a clear spiral. One of the things I've wondered about, is moisture retention. A thin layer of lichen/bryophyte is sufficient to retain enough water to make it look significantly darker than surrounding stone, if it's been a bit windy, and the water on the surrounding rock has evaporated away.

Regarding Stan's rubbing, I think there my have been a bit of relief there when he did them (Though I suspect he does 'enhance' the salient areas of the rubbing), but if it were youghurt induced flora, it probably wouldn't survive long at such a heavily visited site as Castlerigg. There may even be something in the oblique allegation in the article that the acid in blank newsprint (The paper Stan used) may have hastened erosion of lichen, though I'm not so sure it would be sufficiently concentrated to significantly erode the stone itself.