"is there anything possible which can be done in the future to resolve this issue?"
Ethernet ..
One possibility with the boot MCU (PIC18xx) with limited memory is to load code for supporting subdirectories etc.. form the disc itself. Kind of like Compaq BIOS.
The only thing that the MCU
must execute is configuration of the FPGA and KS+WB load. The rest could possible be arranged in other ways.
I hope it's possible to load code into the MCU ram and execute.
