Firmware at the very least. Also looks like the Retail G5 edition (usually) came with 256MB of RAM vs. the 512MB on the Mac Pro card. (Benchmarks show the G5 edition running quite a lot slower than the Mac Pro model on things that shouldn't be CPU limited so there may be differences in core revision/clocking/etc as well.)

You could try digging around and seeing if there's any possibility of flashing the Open Firmware card's BIOS over the EFI BIOS on the X1900 but you may be solidly SOL. (I get a terrible headache every time I try looking up information on flashing cards for Macs, that's why I've never done it.)