There is an inherent safety disadvantage to Design A that would normally make it not allowed in our plant. When torquing the nuts, you could have a galled nut and not realize it. With only one nut to spin and the stud fixed in the case, you would be applying torque, but not properly tensioning the stud. With a pass through stud and two nuts clamping flanges together, you would have to have two failures (both nuts galled to the stud) to have this problem. If only one nut were seized, the other nut would still rotate freely and the stud would still be tensioned by the applied torque.
Johnny Pellin