The ISE board is held in reset when powered on, and the flash is presumably empty to start, so specific configuration cannot be required for this proceedure to work. The interesting parts needed for this to work are the ATU and the Messaging Unit of the i960RP. The ATU is programmed to map the messaging unit registers to the necessary parts of the local address space.
The Messaging Unit has a region of 1004 words that can be used to access local memory. The words starting at 0x50 withing the 4Kbyte register set are index registers that are mapped to local memory.