The problem is, if the titles were syncronised, there would be no recognition of the smaller ones. They would lose their identity so to speak. This is not a bad thing IMO, but if you are running a sanctioning body, it is in your interests to have your title stand out. If a fighter such as Cotto was to hold the WBC plus some alphabet title, the WBC would be the belt being fought for, the smaller one is just passed on by default. It is better for the alphabet body to have a champion of their own. It retains their identity.