I seem to recall reading somewhere that Apple never really optimized the Mac OS to make use of the cool features in the IIfx, while A/UX did make use of them.
If one looks at the IIfx board the IOPs are pretty obvious. The regular I/O chips are there and next to each one is another chip, which has markings on it which indicate it is a custom version of one of the microcontrollers. I can't remember the details at the moment though. Grrrr.