What if we twist your idea around and look at having a Clone-A or NatAmi on a PCI card for UAE to access for custom chip access. (That is assuming that Clone-A or NatAmi FPGA code would be more compatible with the custom chips that WinUAE software emulation.) It sounds like the Clone-A might be.
I think Clone-A was going to be ECS in it's first version but still. I've thought of using modern PC hardware to run Amiga with a PCI card with custom chips for backwards compatibility for years.
-Nyle