Getting PCIe attached SSD to show up as internal drive for BootCamp
Apparently it is not possible to have neither a PCIe flash nor PCIe-attached SSD drive show up as internal on a Mac Pro. I tried multiple PCIe flash and PCIe SATA cards and none showed as internal, even those claiming to be bootable on Mac.

On a side note, even though I could not get FreeNAS (FreeBSD based NAS software) to boot from a PCIe add-on card, I was able to install Windows 8.1 on a PCIe flash drive and it shows up in the boot menu when holding down the Option key as EFI.