Loading custom FPGA binaries from the flash drive (without overwriting the default FPGA image) seems to be a bit complicated. For some crazy reason, the SPI port of the FPGA chip is not hooked up to a SPI port on the STM32. Bitbanging SPI is ordinarily quite simple, but apparently the FPGA expect a minimum steady clock of 1MHz. It would be really interesting to see how this is solved in the bootloader, or if they just ignore the specs.