The firmware updates are only for retail cards. It's very rare that Apple releases firmware updates for OEM cards. Most the the time any firmware patches come in the form of a "ROM in RAM" type patch which loads during startup. The firmware updates are the ATIDriver.bundle and ATIRuntimeDriver.bundle in /System/Library/Extensions/AppleNDRV. If you see a file called ATI ROM Xtender, that's the retail version. It doesn't affect OEM cards.
The firmware update won't do anything to an OEM card when you run the update in a PowerMac. A progress bar may pop up but the second progress bar, which is when the firmware update actually occurs, never pops up. There are better ways ATI could have programmed the installer (such as detecting the OEM card and telling the user it's not doing anything) but at least it won't try and write to an OEM card.