It is not stupid, it is a reality wether you like it or not, it is actually happening. It is not just a 68k cpu, it has its own instruction set, which is totally incompatible with every 68k processor.
Thats true, there are some additional instructions but same goes for the whole 68k family range. Again, if the coder decides to use specific Apollo core instructions he can make a note about it. I dont see a difference if some sw requires 060 or Apollo core aka 080. By your logic all sw should be written for 68000.