If you have a modern board with EFI (a good indicator is a graphical BIOS screen you can use your mouse in) then you have the option of booting in UEFI mode.
This means a slightly faster boot, and means installing windows in UEFI mode. It gives you the option of secure boot, and lets you boot from drives/partitions over 2TB.
If you don't care about that, you can still boot in "legacy" mode. You lose the advantages above.
When the machine boots, it loads either the legacy bios or UEFI bios from the GPU, depending on what is set in the bios. If you flash this card, there will no longer be a UEFI bios, so you'll have to have "load legacy optrom" or similar enabled in the motherboard bios. You may still be able to boot windows in EFI mode depending on the motherboard, but your POST times will be a bit longer and Secure Boot won't work.
UEFI bioses can't be edited by the tool you are using, forcing you to use legacy if you want to mod the BIOS.
My old 7970 didn't have a UEFI bios so I couldn't have secure boot on my z97 board, but I still installed windows in EFI mode. When I switched to 980, I had UEFI, disabled loading legacy roms, and shaved a second or two off my boot time.