I pretty much agree with Higher Thinking.
Chemically, it's perfectly fine to set a rock on top of the substrate.
I just don't do it personally, I like my hardscape to be a bit more stable - I bolt my driftwood to slate, and set it on the bottom, under the substrate (usually I put a thin layer of something protective twixt it and the glass). If I were doing rocks, I'd either set them directly on the bottom, or on top of a brick or something like that if I didn't want them buried that deeply.
I think the hardscape looks better if it's rising out of the substrate, as opposed to just lying on top of it.
Plus it saves you that little bit of substrate that won't be of any use under the hardscape...