Application is an outdoor 30kVA, 480V/400V step down delta-wye transformer to be located within 10 feet of a building panel breaker box. The box has three phase 480V fused power and an input ground wire tied to the breaker box via a screw lug. The output is a 3P4W IEC-309 receptacle, the ground pin of the receptacle has a wire that screws into the breaker box. My question is: Can I use the receptacle ground wire to be the ground for the transformer chassis and X0 of the secondary (via a terminal bar inside and bonded to the transformer enclosure)? Or will I have to run a ground wire independent of the receptacle so that ground is always made regardless of if the plug is in the receptacle. I could not find this detail in NEC.

I suppose you need to back up and see if that transformer is listed for cord and plug connection. If that is OK, I suppose the pin in the plug is sufficient to establish the ground.
Those 309 plugs are designed so the ground makes before the ungrounded pins.

Read 2014 N.E.C. 250.30 (C)

Hmmm, the breaker box is mounted on a metal building. Can I consider the breaker box as the source location? In that case there is a ground wire connected to the breaker box itself (and it comes out via the IEC-309 connector). This is not a permanent installation it will only be active for a month or so.