Yes. Use of Bed-It may not be the best option. The advantage of Bed-It, in my opinion, is in the nature of the product. It is a rubber base that when placed between two mechanical surfaces spreads between the surface, adheres to both surfaces, remains flexible, and releases with manual force without harming either surface.
When using a mechanical screw into a fixed surface, you compromise (too some extent) the ability for the material to adhere to one of the surfaces. This is a problem especially if the temps are low. You are better off using a caulk that is more of a fluid state (like 4200) around the screws. You could make a dam of the Bed-It around the flat base surface of the stanchion. When you screw in the bolts, they will compress the Bed-It between the surfaces (deck and stanchion base) providing extra element to inhibit water intrusion. It is a bit of overkill, but considering water maybe of value.
