At the quarter/roof joint, the factory used lead on vehicles with painted tops, and some type of 'bondo' on cars that were to get vinyl tops. I use a fiberglass reinforced waterproof filler such as 'Duraglas', then finish with conventional filler.
IIRC the drip rail has a lip on it that is spot welded in the window opening. The gap at the roof skin has seam sealer in it.
Dallas