Considering how many pins are on some FPGA chips, making a daughter card similar to Minimig that would have pins around the perimeter may be useful. It may solve for a while the multilayer board making approach.
The older computers like the Altair 8800 had a back plane that connected the processor board to memory,video, etc.
Those board where at 90 degrees to the back plane. These would be parallel to fit into amiga cases.
I do not know what would be needed on the back plane to support the daughter cards. I guess it would be up to the designer.
Making one to fit into old Amigas would be interesting.