I use the latest MMULib libraries instead of the Phase5 libs. :-)
Why? Because they're newer than the Phase5 ones.
And the MMULib 68060.library supports fully the nice mmu.library what the older P5 68060.library doesn't at full functionality. :-)
Cyberpatcher or MuRedox (MMULib tool for same purpose like Cyberpatcher, just different name) only patches/emulates some old FPU commands that aren't supported anymore in the 040/060. It's not done within Setpatch alone itself. Setpatch just looks for 68040.library, if it's present, it loads it and enables access to all 040 functions.
The dummy 040 library just forwards to the 68060.library instead. And is used on older OS3.1 and earlier.
Setpatch from OS3.5 and up also checks for 68060.library, so you don't need to have the 040 dummy library anymore.
My setup here on my A1200 with Blizzard1260 is:
OS3.9 BB2
Setpatch 44.38
68060.library 40.18
mmu.library 43.6
MuRedox 40.4
My system is running fine and nice. I can even say it's rock-stable ;-)