Dual SPI master with ATmega32u4
You might want to take a different approach altogether. Instead of attaching both the PROM and the FPGA to the &micro;C as slave devices, attach the PROM directly to the FPGA, and allow the FPGA to boot in SPI master mode instead of SPI slave mode. Bonus: the booting will happen more quickly.

You'll still be able to access the PROM from the &micro;C after the FPGA has booted for firmware updates or data storage, by passing the &micro;C's SPI interface signals through the FPGA logic.