To understand why you need to learn more about the Hierarchy simplification.
When it was necessary to change the client settings for an area or inventory settings you had to change the SMS_DEF.mof at the primary.
Now with 2012 you can create client settings and special Inventory settings. Then you assign it to a collection. Depending on which collection it is in, the machine will recieve a differnet policy or Inventory settings. To control which one it will recieve you can change the priortiy level of each custom policy settings.
