The admin/panopoly/libraries/pages Overridden Page Templates contains all of the panelized contents, not only the overridden. We have default panes set up on content types, so creating new entity always generates new record in panelizer_entity table.
As I figured, the difference between the overridden and default the did value on panelizer_entity table:

If I am right, we need a ->condition('pe.did', 0, '>') in panopoly_admin_overridden_page_templates_content_type_render()
function panopoly_admin_overridden_page_templates_content_type_render($subtype, $conf, $panel_args, $context) {
// --- some stuff ----
$pages = $query
->fields('pe', array('entity_type', 'view_mode', 'entity_id'))
->orderBy('pe.entity_id', 'DESC')
->condition('pe.entity_type', $entity_types)
->condition('pe.view_mode', 'page_manager')
->condition('pe.did', 0, '>') // <--this
->execute()
->fetchAllAssoc('entity_id');
foreach($pages as $overridden_page) {
Comments
Comment #1
beeradb commentedI can confirm this is the case. If you have multiple allowed default panel layouts the node will show as overridden regardless of the actual state. The did check does look to fix it.
Here's the patch.
Comment #2
populist commentedAwesome
Comment #3
szantog commentedIt seems, a ->distinct() is also missing,
I get this list: http://www.diigo.com/item/image/2peqe/367s?size=o
Sorry, if I don't file patch, the environment, within I'm working, it is hard to make patches.
Comment #4
populist commentedMakes sense. Added it up!
Comment #5.0
(not verified) commentedtypo