The obvious idea is to have a single FPGA board with RAM, large enough to hold the full AGA/OCS/ECS/RTG/CPU cores, and have a I/O connector. This could be produced in large numbers and would be quite small.
Then do smaller production runs of a separate "Connector boards" that match up to the various cases, and these "Connector boards" would hook up to the FPGA board's I/O connector! simple.
This would allow users to replace broken motherboards easily.