It is impossible to be more compatible with an 040 than an 040, any deviation from an 040 makes it less compatible. It might run software that wouldn't run on an 040, but that is a different thing. oxypatcher/cyberpatcher/etc already solved the problem of emulated instructions years ago. So being more compatible in your sense isn't even true.
What's being referred to here, I believe, is the option of being able to implement all instructions directly. FPU instructions which existed on the m68881 / m68882 but not on the m68040 can be built in to the FPGA, so exception traps don't need to run (which are much slower). Likewise, there'd be no sense in installing trap handlers for instructions missing in the m68060 if one had reasons to pretend to have an '060.
While a ROM and/or library can be loaded for trap handling (so from the OS point of view you're running as if you're on a real m68040), the code would just never get used. You could have complete systems which could move between a real m68k processor and an FPGA emulated superset processor without any compatibility issues.