As far as I got the discussion, a CPU library is not even required. Thus, if the core sets its reserved bit, SetPatch should not even load a CPU library in first place.
First: Thank you for replying

Yes, according to the Vampire developer Gunner von Boehn a 68040 library should not be needed. However for some reason OS3.1.4 gives the missing library error after install and will not boot WB. The only way to solve this - so far - has been either to comment out CPU CHECKINSTALL in the startup sequence OR installing an old 68040 library.
Some say commenting out CPU CHECKINSTALL causes other problems and should therefore not be done. Others say that is the best way. It is a choice between two evils ATM to get past the error. What is your opinion on the pros and cons on both methods?