Simple issue of Production Serialization

The terminology you are using doesn't make sense here. "Serialization of FPGAs" could mean a lot of things. I think what you are trying to do is attach a unique ID of some kind to each FPGA or each board.

Presumably you've got some flash part that you are using to store the FPGA image that is loaded on bootup. Could you not just write a value into that flash. You could also add an eeprom to the board which you program with the unique ID during production which can then be read by the FPGA.

In several of our products we have to store a MAC address on the board. I typically write a little program that the production house uses which programs the MAC address into the board and increments it for the next board. The mechanisms I use to program the MAC address vary but basically I download a little test program into the FPGA which allows me to send the data to the FPGA either via JTAG or some other path.

Jake