I think the rubber would work better than silicone or caulk, as it will allow for more "working" of the stanchions and still stay watertight. Water getting in through the bolt-holes seems to be a big source of rot...
5200 placed into the holes then the screw inserted would seal out any moister. It would also prevent loose screws from happening. Gaskets rot in the elements and screws loosen.
The 3M 5200 is good for a more permanent fix. We use the 5200 to secure/seal the Berkley jet pumps in the hull. Flexible but extremely tough stuff. Now the 3M 4200 is workable to the point you can "undo" what you've sealed.