What you described is a three phase 4 wire system. You happen to not be using the neutral for any loads but is still the grounded point of the system. All ground fault current will return to the XO terminal of the transformer regardless of what other items it finds a path through on it's way there.
All that content of 610.61 mentioned in OP is about is assuring there is a bond around the trolley in case there is too much resistance between the crane and the frame. If whatever cable method you have between crane and frame for the supply conductors contains a fourth conductor used as an EGC, that will make up the bonding jumper, they just don't want to rely on the trolley to have to provide low enough resistance to be effective ground fault path.
I am asking because I really do not know, why would one not terminate the EGC to the EGC terminal at the transformer frame along with the supply primary and secondary EGC's? I understand the concept that some of the fault current will go to the XO but would you not have loss from the xo? I was under the impression you wanted a clean path back to the source to open the breaker or fuse.?