Using CMD on Very Old PC Keyboard During Boot
Unfortunately I think you're out of luck. I don't know exactly what sorts of tweaks you've used to get a command key in OS X, but they're almost certainly at the OS level, not on the hardware or firmware level. The EFI boot loader can't read these tweaks, so unless the keyboard itself can directly send the command key signal, you're out of luck.

The only thing I can think of is some sort of hardware device that would stand in between the keyboard and the Mac and spit out modified key codes if given the proper input. However I don't know of any such product. Perhaps something could be hacked up using an Arduino or something similar, but it would be a fairly substantial project.

I think you're best off just getting a cheap keyboard with a windows or command key and keeping it in a drawer for the few occasions when you do need it.