Even the 68k version of 3.9 causes all kinds of issues on a real Amiga. I have a CSPPC/060 and it didnt run correctly. Cost me hours of attempting to get it stable with the only result in a new install of OS3.9 and putting back MUI 3.8 again.
I dont think this is intended for real Amiga machines. Its more geared at Amikit and UAE systems. Sadly WinUAE has caught up and in just about all cases now is faster than the real thing with better resources.