Currently when exporting / publishing a site there is a section called "Application Configuration" that allows you to export the application settings for each of the applications being used in that site. However, some of the applications have site-wide configuration while for some others the configuration is per instance. The site administrator has no way to tell the difference and that's problematic.
LPS-43134 it is now possible for an application (a portlet) to have both site wide and portlet instance setting configuration, which adds to the potential confusion.
In order to solve this, the proposal is to move the site-wide configuration along with the list of applications under the Content section. This is consistent with the fact that going forward all site-level settings will be set from Site Administration through each application entry.
The application instance settings should be moved to the pages dialog since they are very tied to the pages. However, we don't think these options are useful so they should be considered deprecated and disabled by default with a portal property.