I'm betting that the whole use of Zorro like slot, reference to custom chips, joystick port tease and at teh aeon site.. when you type AA, AGA, AAA in the script popup over the slots suggests that there is somekind of legacy board that plugs in there. Jenns isn't the only person that has worked on an FPGA Amiga clone project. With te open source nature of Minimig it's not a stretch that somekind of legacy solution has been found.
I'd be hapy with a Rock solid WinUAE implementation.