There is no need for through-bolting. On a deck stepped mast the load is straight down on the plate and the lateral forces are low. Deck stepped masts are held in place only by the lip of the plate; I know my mast doesn't have any screws or bolts holding it to the plate.
Since you filled the original holes with epoxy, once you drill them out again for the proper screw size you will be good. No need to through-bolt; but if you are doing other repairs that make it possible and can cover everything up, there's certainly no reason not to go the extra mile.
S/V Free Spirit
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