Filling in the cracks is definitely recommeneded. Though the cause is more of a concern. Since the problem will re-occurr. Make sure the shrouds are not over tensioned. This would be a contributing factor to seeing those cracks at the mast base.
If there is coring around the stanchion I would over bore the hole then remove some of the core and reset epoxy to cover the larger hole. Then drill for the new bolts. Rest assured they will never leak or cause you a problem is done properly.