I like B - My thoughts are suspend it under the roof top tent with 2 long pieces of C channel going from front to back. Put a stopper of some sort on the front and a removable keeper at the back. Simple slide it in thru the rear. Some sort of security is necessary.
You could also build a basic box out of 1/4" plywood. Simply bolt it to the bottom of the Thule rack. Spray it with a black bed liner product. My guess is the box would weight 15 pounds.
Looking forward to seeing what you come up with.
2013 Jeep Wrangler Rubicon