Если речь идет о записи самой SPI флешки, то ответ дан на той-же станице:
Bypass the FPGA and use the FT2232 as a JTAG/SPI/MPSSE Programmer
The Papilio Pro provides the JP4 pin header, jumping this header will hold the Spartan 6 FPGA in a reset state which frees up the JTAG pins to be controlled by the FT2232. OpenOCD, FlashRAM, and any other FT2232 based software should work directly with this method.
Т.е. замыкаем и используем FlashRAM для записи SPI.
