to make sure your pipeline doesnt break when updating plugins. pyblish config only overwrites settings it finds in the settings file it leaves everything else at default value.
example: a plugin has various attributes. the json only contains a single attribute, node_type = "mesh" all attributes of the plugin will remain the same except for the node_type.
the exception to this is the plugins registered. it will only use plugins matching the plugin names in the settings file
example: you have 5 plugins registered. the settings file has 3 plugins listed. only those 3 plugins will be used.
See the config creator, a little qt helper tool to help you create configs. (still in alpha, will have bugs)