The A casing might need to made bigger and stronger to be able to include the holes for the studs?
Many people are a bit wary of studs because if one breaks or you don't get it inserted right then you're in a world of pain, where as with a flange, stud and nut you can just throw it away and start again.
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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.
Design A may be cheaper to manufacture since it requires less welding (weld inspection, stress relieving, etc.) as long as the case is thick enough to take the threaded holes. I think all API machines would require flanges and would tend to be more expensive as a result.
