Is it possible to have one version single core, and then slowly migrate the software to multi-core? You could dual boot either version.
Otherwise there is sandbox mode like a Java Virtual Machine.
Would it be possible to invoke each 68k/PPC AmigaOS program in its own environment, a sort-of emulated AmigaOS instance in the vein of a VM? Instead of each instance being isolated to its own virtual environment, having the virtual AmigaOS instead be "patched" with wrappers which would allow the AmigaOS VM to communicate with the host OS and other AOS VMs?
In this manner, the host OS could be designed as SMP with memory protection, while still offering backward compatibility to existing AOS software. At least in my mind. I'm curious to know how Apple had OSX run MacOS 9 software natively.