Trust me, regions are no where as autonomous than in England,France and Spain for that matter.The local officials can give false reports to the emperor but can't actually defy them if an edict has been drafted.In case you don't know, the Ming Dynasty actually has MULTIPLE MASSIVE secret police networks throughout the entire empire implanted in various ranks of local governments,army units as well as within the populace itself.The secret police organizations include:Jinyiwei,Eastern Depot and Western Depot.
Regardless, there are reasonable historical reasons to put a minimum on Ming's local autonomy and not on England's, France's, and Spain's local autonomy. Though it's a matter of speculation what might have happened if the Ming tried to dramatically change their administrative and economic policies, it's not unthinkable that serious reform would have been on par with what the Westernization process currently entails, meaning many years or even decades of revolts and finally having a practically entirely different type of government without any local autonomy penalties, and less minor reforms would be on par on with idea bonuses.