A semiconductor wafer stocker apparatus includes a body frame, an inlet port to load a wafer shipping box into the body frame, an outlet port to unload the wafer shipping box from the body frame, an automated transfer robot operable to convey the wafer shipping box between the inlet port and the outlet port, and a shelf module within the body frame. The shelf module includes a shelf plate configured to support the wafer shipping box. The shelf plate includes first, second, and third protruding support pins arranged to align with respective grooves in an underside of the wafer shipping box and orient the wafer shipping box with a door thereof facing away from the body frame. The first and second support pins may be closer to the body frame than the third support pin. Related apparatus and methods of operation are also discussed.