You can recess the trim with spade bit for the bolt heads. There are spade bits with short pilot so that you don't punch through the trim. Wider bit would give you room for adjustments. Dremmel or router would make that easier.
I see a lot of rotting facia because they were nailed directly to the lumber. No drain/air space. I would plan the deck so that I could use 1/2" cleats between the lumber and the finish, which also takes care of bolt heads.
I see a lot of rotting facia because they were nailed directly to the lumber. No drain/air space. I would plan the deck so that I could use 1/2" cleats between the lumber and the finish, which also takes care of bolt heads.