So I have a MacPro 1,1 and have recently purchased and EVGA GTX 680 2GB, I am just wondering, if I flash this card and am running OS X 10.11, and therefore have a boot.efi which is technically EFI64, will I get boot screens from this card on my Mac?
Yep, what @Robert Davies said, your Mac still has 32 bit EFI, it's just "calling" 64 bit OS through modified boot.efi file.
Also, nVidia with Mac EFI will give you 2.0 PCIe speeds in Bootcamp (you'll get them in OS X through web drivers), but since 1,1/2,1 have only PCIe 1.1 slots, there is no gain in that either.
Use it as a PC card and all will be ok. I've spent too much time on HD6850 EFI rom before i realized it is 64bit