I believe the missing part to get any accelerator working on Macs is timing/arbitration related to interfacing with the rest of the hardware. That's most likely why stuff like floppy and SCSI have some issues working.
If you just want to run software, but faster, without original hardware, then using a software emulator like Basilisk II is fine.
However, a lot of the reasoning for using newer accelerators with older hardware is that you want fast speed or want to attach newer hardware, but still want to use your existing SCSI drives, ADB mouse/keyboard, NuBus cards, floppies, the case/screen ...
Since there are very many Mac models each with different timing characteristics and different ROMs, it may be very time consuming and very difficult to get them all working easily since timing needs to be figured out and ROMs need to be patched.
A suggestion for another way to possibly work around timing issues is to have the original CPU act as an "I/O processor" which then communicates with the hardware on the accelerator over the PDS slot.