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Two things I have found is when the top wood is correctly manufactured and correctly installed, -AND if the correctly shaped top moulding is used, they do not need any type of sealer to keep from leaking under normal usage.
With that said, I suspect if you are experiencing issues, then one or any combination of these items listed above is your issue. So at that point, I suppose you are going to want to use something that will flex with the body while being driven, ...especially if the top wood is installed incorrectly and allowing the sheetmetal to flex. One word of caution is that Silicone per se' is generally not the ideal sealant due to the acidic nature of it around unprotected sheetmetal. Might I suggest considering using Seam Sealer that is generally found at auto body supply stores. It comes in colors and can also be painted if desired.
BTW, seeing this is your first post, welcome to Fordbarn!!