I would suggest reading the original Motorola data sheets for the 68k CPU family. I've looked at it a little and it sort of made my head hurt. The answer to whether those pins are important or not in a given hardware design seems to be a great big fat "It Depends". Function codes are an integral part of how the m68k handles distinctions between user and supervisor mode, and it appears from skimming the manual it would in theory be possible to design a 68k computer which used up to *eight* separate 32 bit address spaces for different priority software and use the output of those function pins in any number of ways to enforce security.
The one succinct explanation I did see about the workings of those pins implied that normally they were used by the MMU and that the physical memory subsystem doesn't necessarily need to care about them. (IE, the MMU will do the job of comparing the function codes to the translation tables it maintains and allow or deny access at that level.) It *may* be that the only reason the 68030 has the pins brought out despite having a built-in MMU is to allow the chip to be used to upgrade older designs with proprietary memory management systems. (At first glance the pins appear to be absent on the 68040 family.) But, really, I have no idea whether a Mac cares about them or not. To my knowledge the classic MacOS uses supervisor mode exclusively so I don't know under what circumstances those pins would even change state. (Under A/UX or NetBSD it's another story.)
The one succinct explanation I did see about the workings of those pins implied that normally they were used by the MMU and that the physical memory subsystem doesn't necessarily need to care about them. (IE, the MMU will do the job of comparing the function codes to the translation tables it maintains and allow or deny access at that level.) It *may* be that the only reason the 68030 has the pins brought out despite having a built-in MMU is to allow the chip to be used to upgrade older designs with proprietary memory management systems. (At first glance the pins appear to be absent on the 68040 family.) But, really, I have no idea whether a Mac cares about them or not. To my knowledge the classic MacOS uses supervisor mode exclusively so I don't know under what circumstances those pins would even change state. (Under A/UX or NetBSD it's another story.)