It seems to me that the comment about the wedge case being more valuable than the hardware inside holds some truth. Since that is the case, it would make more sense to make an FPGA based motherboard replacement.
I know, not enough market. BUT since the FPGA based systems are so much smaller, the answer isn't to make a custom Amiga format board. The solution is to make an adapter. That is what I did with the MiniMig case I am finishing up now. I picked out my case, which happened to be an external USB DVD/Harddrive case. I installed all of my ports in the case with cables to the actual ports on the MiniMig. The only barer to putting an existing MiniMig in an Amiga wedge case is the placement of the SD card, which I was advised not to try and cable out, and the fact that the mouse and keyboard are PS2.
While they would take SOME effort, the mouse and keyboard should not be too much of a technical feat to get past.
Using this I don't see any reason that the MiniMig, or ReplayArcade could not be put in an original Amiga case.