Rebedding Stanchions by bonding hardware with epoxy

So, I have to remove and rebed a couple of stanchions and the last Sailor Talk really got me to thinking about how I want to do it.  I definitely want to fill the through deck holes that currently hold the stanchions in place with epoxy and try one of the solutions described here:

However, if anyone out there has done this with their stanchions I have some follow-up questions. 

First, I really like the idea of the threaded stud so that I can just tighten a nut on the stanchion to hold it down.  In the description on the epoxyworks site, it shows a solution that allows the stud to be removed later.  Does anyone know what the downside to just using an inverted hex-head bolt and not worrying about removing it later?  Is it in case you screw up the threads somehow?

Secondly,  the instructions suggest you leave a nut so that it is proud of the surface.  Does this create issues for  whatever seal you use around the base?  According to sites I have read, you should not use 5200, but 101 or some other sealant.  

Lastly, my current stanchion seem to have some kind of rubber gasket, is this necessary or preferable to 101 or some other caulk, or is it used in addition to those?

Any suggestions or help would be appreciated.