The Panelizer menu items were added to the Configuration section because that matched where they originally were in the old Drupal 6 version. Since then their settings have become substantially more elaborate and it no longer made sense for them to be there. The Panelizer settings have now been moved to the Structure section of the administrative interface, alongside the main Pages (Page Manager) and Panels menu items.
Site builders should be aware of the new location of the menu items. Module builders should be aware of them for any custom integration they build for their modules, e.g. support for new entities, etc.