Why not make it more or less like a sleeping bag, only larger?
If it can be velcroed closed it might be lots warmer that way, especially if he is the type who twists and turns during his sleep.
You could make it sleeping bag like except fit the bunk bed and look good.
I know when we used to go car camping (with station wagons, remember them?) we finally got rid of quilts and went the sleeping bag route. It was simply too hard to keep warm when one or more of us were twisting and turning during a windy, cold night.