i don't see why you couldn't. once that stuff sets it does a good enough job of holding things in place, but i don't know that it would work as well as drilling for rods or hydraulic cement.
just don't make your rock structure in to super huge monolithic pieces. you may want to move/change it at some point.
the only down side i can think of off hand is that it would be almost impossible to remove. whereas with the epoxy or hydraulic cement you can chip it off, silicon has an infuriating way of working itself in to every little crevice and staying there for all eternity.
i bought a used tank a while back where the previous owners had siliconed the bulkheads in to place for the RR drains. it was a major PITA to remove, even on glass. took me a good two hours laying under it with a razor blade, and there was still a light film i couldn't quite get off.