The bolts on Harmonie are Flat head machine screws, M8-1.25 x 30mm I see no evidence that they had ever been removed since the boat was built in 1996.
We are very much on the same page with thinking about the issues/concerns in getting those bolts sealed back up. If you read Joel's notes he does mention adding sealant under the stanchion base in addition to the tef-gel on the threads. Done properly, that should keep the water away from the steel.
I think the combination is much better than just putting a dab of silicon on the screws as was done on my boat.
Here is my approach:
Each bolt hole will have a chamfer cut into the surface of the fiberglass with a countersink bit.
The bolts will have a thin coat of tef-gel added to the bottom couple of threads. I might just put some down in the bolt hole to minimize contact with the upper threads--for all the reasons you expressed. Another alternative is to apply tef-gel to a screw, insert it all the way in the hole to smear the tef-gel on the female threads, then remove it and use a clean screw for final assembly.
The bottom of the stanchion base will have a layer of butyl sealing tape applied, with a little more wrapped around the bolt at the very top of the threads.
Butyl tape "flows" amazingly well. Even if the threads of the bolts have a bit of tef-gel on them, I am confident that the butyl flowing into the chamfer I made at the top of the hole will be good enough to keep water out.
This basic technique has worked well for me in the past in similar situations.
Annapolis, MD, USA