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Seems to me the prep is more important than what sealant you choose. Even the best sealant isn't going to hold up if there are excessive gaps or an infirm fit. I would recommend a fiberglass riser plate epoxied to the deck under the base as Guy has described before. 1/4 to 1/2" would do. It spreads the load and lifts the seal area up above most of the flowing deck water (like rain water, not when you dip the rail). Removing core around the holes and filling the void with epoxy is a must for good sealing. I like to tap the holes for the 1/4-20 fasteners (or 6mm if you're doing this in Europe). And have a proper bevel at the top of the hole to hold sealant. The mating surfaces between the stanchion base bottom and the deck or riser plate surface should be clean and smooth and well matched.
These are all basic techniques to the process that have been discussed here many times.
Apply these techniques and the choice of sealant is secondary. That said, I would choose polysulfide over silicone or polyurethane. Boat Life Life Caulk or 3M 101. The silicone is amazing in that it won't stick well to anything and yet you can't get the residue off. The polyurethane is forever glue (5200 and to a lesser extent 4200). And when these start to leak down the road (and they will start to leak) it's much harder to re-do. I like butyl but you need to be careful that fasteners don't spin where you need the seal or you twist it up too much.
Dan Pfeiffer