Epoxy weight in hole. Yes it blocks the through hole. Let dry. Using battery drill and 1/8 or smaller drill you redrill the weight. The only weights that come predrilled are in the Cowboy and sandeel swimmer kits and it's because of thickness.
Sealing doesn't plug up any holes. At least it shouldn't. There shouldn't be that much sealer in a lure left over it will next dry in that thickness.
Rattles get mortised into the belly of the lure, either by hand or with something such as a dremel tool. Epoxy it in so it's roughly flush to the diameter of the lure, then fill with wood filler or bondo to make it invisible (if you don't want to just paint over it)