The FPGA Arcade is just a new version of the MiniMig with a bigger FPGA and more expandability. The FPGA code running on it is essentially the same with a few perks added (such as AGA implementation). The original MiniMig is made obsolete by this board so I wouldn't call it a separate project. It's more like a sequel to the original MiniMig.
The Natami team offered to let the MiniMig/FPGA Arcade team use code from the 68050 subproject but I don't know if the closed-source license scared the MiniMig/FPGA Arcade developers off or what the deal is there.
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1500 posts for me! Yay!