I didn't find the soul coins in the ruins before the latest patch, although I may just have overlooked them. Anyway, I wondered whether their presence represented some sort of burial for the owners of the souls.
As for things being out of order, I believe some folks head straight for the grove instead of clearing the ruins first, so there may not be a "right" place to explain their value. I can't remember whether or not the first copy of the soul coin book was in the ruins.
