Interior and Exterior handrails bolted together
I have the same arrangement on my Luders 33 and it was leaking badly. I removed all handrails and will not replace the ones inside – when healing, I find it easier to hold on to the sides than the ceiling. If you do that, you’ll need shorter bolts. But if you prefer to reinstall the inside ones, the threaded rod is the way to go.
Anyway, since you are at it, I would to do what I did: drill the holes with a bit the same diameter or slightly bigger; countersink the deck side of the deck hole; clean the inside with acetone then stick a piece of duct tape on the ceiling inside the cabin making sure it is well stuck. Mix epoxy without any filling and pour on the hole. Put a cup or a plate under the tape inside and remove the tape draining the epoxy which can be re-used. This will ensure you are protecting your deck from future moisture problems. Then when the epoxy is cured make sure you re-bed the outside rails with butyl tape from Maine Sail.
Good luck on your project.