It's because the firmware is different would be my guess. It's a different SKU, slightly different firmware, so the BIOSes for the 3998, while they will work with the 3999 (most likely), you'll have to manually do it with NVFlash because the provided tools to update the ReBar BIOS or any of that probably won't work for the 3999 that are designed for the 3998.
Kinda silly, but it is what it is - same thing happened with the 3090 FTW3 Hybrid vs regular cards - not sure if it's the same way for FTW3 vs Hybrid vs HC, since the HC regular 3090s/3080s are rare a-f right now.