The problem with using silicone to glue rock structures together is that unless you have a lot of surface to bond together, the silicone is very weak. It's like, if you took two pieces of glass, put a glob of silicone on the flat side of one piece and smooshed the other piece down on that, you'd be hard pressed to ever get them apart again without breaking the glass once it cured.
On the other hand, if you used the silicone to glue them together perpendicular to each other, you couldn't manage to get it to stand upright, let alone stay glued together. Same problem with rocks, they usually have very irregular surfaces, so a putty with strong bonding properties is going to work much better than a gel with weak bonding properties. The putty fills the spaces and bonds the two stones together, much like mortar cement, but with easier workability and a quicker cure.