You don't mention and pics aren't clear where exactly these holes are. You offer some interesting ideas, but I think you're overthinking this. When seats were removed from my previous B700, I filled them with clear silicone, obtainable at any auto parts store. Those bolts weren't much bigger than 3/8, if they even were bigger. Smeared an inch or two out from, and built up properly in/over exterior roof holes, clear silicone should keep the elements out as long as the exterior surface surround any outside hole is cleaned prior to filling.
"Cheese Wagon" <email@example.com>
Former owner - 1989 Ford B700 64-pass Blue Bird (Rest In Peace, Cheese Wagon)