This goes back before me, but it is my understanding that the (what is now) USATF certification process was instituted because the organization wanted to keep road race records and a major factor in whether a record was set was whether or not the course was at least the distance it was advertised to be.
Over the last almost thirty years the reasons have evolved. Records are still set, but race participants have begun to trust the "USATF Certified" "brand" as an almost certain indication that the course is properly measured start to finish, and that the intermediate points are the right distance from the start, finish, and each other.
If we limit the use of the "brand" to the smaller number of races that see an advantage in USATF sanctioning, my fear is that fewer races would seek certification, thus fewer courses would be accurately measured, and the quality of the sport, as measured by the quality of its events, would suffer.
If USATF insists on this, I would suggest we look into a more formal alignment with another group- such as RRCA.