ChuckFan, the first part of your question I can't help you with. Logic would seem to demand a somewhat sturdier topgallant mast if the royal were to be set above the topgallant. The second part, however: "set flying" describes the work of setting a sail already bent to its yard. The topgallant, bent to the yard, would be hoisted to the truck of the royal mast in this case, as opposed to, say, the topsail, which would be bent to a standing yard and furled, dropped or shortened (reefed) while the yard remains crossed on the mast. Most "kites" (skys'ls, moons'ls, cloud pokers) would have been "set flying."
Best,
Ron Mariner