Now I got what you was looking for. I don't think that is so simple by just bringing out more pins from the FPGA. It will require additional electronics to make it compatible (the MiniMig runs at 3.3 V internally for example) and to make it robust (you don't want to blow the FPGA by bad hardware or stupid usage). Also, it will not make the MiniMig mini anymore, taking away the original intention of the design.
My idea with pin headers was more to make it possible to create add-on modules for custom applications, not only for Amiga usage. But, as I said before - in this design, I have put reliability and performance as top priority without bringing the costs too high.