Only in node_pane_patched/js: node-pane.entity-bundle.js
diff -ur node_pane_dev/node_pane.info node_pane_patched/node_pane.info
--- node_pane_dev/node_pane.info	2013-10-01 04:25:01.000000000 +0200
+++ node_pane_patched/node_pane.info	2015-10-13 17:12:55.000000000 +0200
@@ -10,3 +10,18 @@
 project = "node_pane"
 datestamp = "1380594301"
 
+; Patches
+; https://www.drupal.org/node/2065005
+; https://www.drupal.org/node/1859374
+
+; Changes
+; - Added a admin UI section on each content type to define how it content can be administered:
+;     [ ] Use in 'Panels'
+;         [ ] Select existing content in panels
+;             [ Select the selection view ] => defaults to node_pane_selection
+;         [ ] Create new content in panels
+;
+; - Added check if user is allowed to create content, if not the "Create new <content-type>" is removed.
+;
+
+; drupal_alter('panels_ipe_pane_links', $vars['links'], $context);
\ No newline at end of file
diff -ur node_pane_dev/node_pane.module node_pane_patched/node_pane.module
--- node_pane_dev/node_pane.module	2012-03-14 16:56:31.000000000 +0100
+++ node_pane_patched/node_pane.module	2016-01-05 12:46:00.000000000 +0100
@@ -23,35 +23,53 @@
   $ctools_content_types = array();
 
   foreach(node_type_get_types() as $name => $node_type) {
-    $ctools_content_types[$name] = array(
-      'title' => t('New @type', array('@type' => $node_type->name)),
-      'description' => $node_type->description,
-      'category' => array(t('Content')),
-      'add form' => array(
-        'ctools_node_content_type_add_form' => t('Add new @type', array('@type' => $node_type->name)),
-        'ctools_node_content_type_edit_form' => array(
-          'default' => TRUE, // put wrapper here, not on the previous form.
-          'title' => t('Configure display'),
-        ),
-      ),
-      'edit form' => 'ctools_node_content_type_edit_form',
-    );
-  }
+    if (node_pane_access('use_in_panels', $node_type->type)) {
 
-  // Add an existing node.
-  $ctools_content_types['existing_node'] = array(
-    'title' => t('Choose an existing content'),
-    'description' => t('Add a node from your site as content.'),
-    'add form' => array(
-      'ctools_node_content_type_selection_form' => t('Choose an existing content'),
-      'ctools_node_content_type_edit_form' => array(
-        'default' => TRUE, // put wrapper here, not on the previous form.
-        'title' => t('Configure display'),
-      ),
-    ),
-    'edit form' => 'ctools_node_content_type_edit_form',
-    'category' => array(t('Content')),
-  );
+      if (node_pane_access('select_in_panels', $node_type->type)) {
+        $ctools_content_types['existing_node_' . $name] = array(
+          'title' => t('Choose an existing @type', array('@type' => $node_type->name)),
+          'description' => t('Add a @type from your site as content.', array('@type' => $node_type->name)),
+          'add form' => array(
+            'ctools_node_content_type_selection_form' => t('Choose an existing @type', array('@type' => $node_type->name)),
+            'ctools_node_content_type_edit_form' => array(
+              'default' => TRUE, // put wrapper here, not on the previous form.
+              'title' => t('Configure display'),
+            ),
+          ),
+          'edit form' => array(
+            'ctools_node_content_type_edit_node_form' => t('Edit @type', array('@type' => $node_type->name)),
+            'ctools_node_content_type_edit_form' => array(
+              'default' => TRUE, // put wrapper here, not on the previous form.
+              'title' => t('Configure display'),
+            ),
+          ),
+          'category' => t('Content'),
+        );
+      }
+
+      if (node_access('create', $node_type->type) && node_pane_access('create_in_panels', $node_type->type)) {
+        $ctools_content_types[$name] = array(
+          'title' => t('New @type', array('@type' => $node_type->name)),
+          'description' => $node_type->description,
+          'category' => t('Content'),
+          'add form' => array(
+            'ctools_node_content_type_add_form' => t('Add new @type', array('@type' => $node_type->name)),
+            'ctools_node_content_type_edit_form' => array(
+              'default' => TRUE, // put wrapper here, not on the previous form.
+              'title' => t('Configure display'),
+            ),
+          ),
+          'edit form' => array(
+            'ctools_node_content_type_edit_node_form' => t('Edit @type', array('@type' => $node_type->name)),
+            'ctools_node_content_type_edit_form' => array(
+              'default' => TRUE, // put wrapper here, not on the previous form.
+              'title' => t('Configure display'),
+            ),
+          ),
+        );
+      }
+    }
+  }
 
   return $ctools_content_types;
 }
@@ -70,10 +88,12 @@
  */
 function ctools_node_content_type_selection_form($form, &$form_state) {
   // add a default view as form prefix for selecting the content
-  // get the view name from a variable, to make it possible to provide a
-  // different view
-  $view_name = variable_get('node_pane_selection_view', 'node_pane_selection');
-  $form['#prefix'] = views_embed_view($view_name, 'default');
+  // the view is set through the content type admin ui.
+
+  $view_name = variable_get('node_pane-select_in_panels_view', 'node_pane_selection:default');
+  list($view, $display) = explode(':', $view_name);
+
+  $form['#prefix'] = views_embed_view($view, $display);
   if(!empty($form['#prefix'])) {
     // switch from text input element to hidden
     $form['selected_nid'] = array(
@@ -104,15 +124,36 @@
 }
 
 /**
+ * The form to add or edit a node as content.
+ */
+function ctools_node_content_type_edit_node_form($form, &$form_state) {
+  $conf = $form_state['conf'];
+
+  module_load_include('inc', 'node', 'node.pages');
+
+  $node = node_load($conf['nid']);
+
+  $form += node_form($form, $form_state, $node);
+
+  // Remove the submit and preview buttons.
+  $form['actions']['#access'] = FALSE;
+
+  $form['buttons']['next']['#submit'][] = 'node_pane_content_type_add_form_return_submit';
+
+  return $form;
+}
+
+/**
  * Add form for node panes.
  */
 function ctools_node_content_type_add_form($form, &$form_state) {
   global $user;
+  global $language;
 
   module_load_include('inc', 'node', 'node.pages');
 
   $type = $form_state['subtype_name'];
-  $node = (object) array('uid' => $user->uid, 'name' => (isset($user->name) ? $user->name : ''), 'type' => $type, 'language' => LANGUAGE_NONE);
+  $node = (object) array('uid' => $user->uid, 'name' => (isset($user->name) ? $user->name : ''), 'type' => $type, 'language' => $language->language);
 
   $form += node_form($form, $form_state, $node);
 
@@ -134,3 +175,116 @@
   $form_state['conf']['nid'] = $form_state['values']['nid'];
 }
 
+/**
+ * Function to determine if a node type can be used for node pane selection.
+ *
+ * @param $access
+ * @param $type
+ *
+ * @return boolean
+ */
+function node_pane_access($access, $type) {
+  $permission = variable_get('node_pane-' . $type . '-' . $access, FALSE);
+  return $permission;
+}
+
+/**
+ * Implements a delegated hook_form_alter.
+ *
+ * We want to add Panelizer settings for the bundle to the node type form.
+ */
+function node_pane_form_alter(&$form, &$form_state, $form_id) {
+  if ($form_id == 'node_type_form') {
+    if (isset($form['#node_type'])) {
+      $bundle = $form['#node_type']->type;
+
+      $settings = array(
+        'use_in_panels' => variable_get('node_pane-' . $bundle . '-use_in_panels', TRUE),
+        'select_in_panels' => variable_get('node_pane-' . $bundle . '-select_in_panels', TRUE),
+        'select_in_panels_view' => variable_get('node_pane-' . $bundle . '-select_in_panels_view', 'node_pane_selection:default'),
+        'create_in_panels' => variable_get('node_pane-' . $bundle . '-create_in_panels', TRUE),
+      );
+
+      $form['node_pane'] = array(
+        '#type' => 'fieldset',
+        '#title' => t('Node pane'),
+        '#collapsible' => TRUE,
+        '#collapsed' => FALSE,
+        '#group' => 'additional_settings',
+        '#attributes' => array(
+          'class' => array('node-pane-entity-bundle'),
+        ),
+        '#bundle' => $bundle,
+        '#tree' => TRUE,
+        '#attached' => array(
+          'js' => array(ctools_attach_js('node-pane.entity-bundle', 'node_pane')),
+        ),
+      );
+
+      $form['node_pane']['use_in_panels'] = array(
+        '#title' => t('Use content type in panels'),
+        '#type' => 'checkbox',
+        '#id' => 'node_pane-use_in_panels',
+        '#default_value' => !empty($settings['use_in_panels']),
+        '#description' => t('Enables this content type inside the "Content" category of the pane selection dialog box.'),
+      );
+      $form['node_pane']['select_in_panels'] = array(
+        '#title' => t('Select existing content in panels'),
+        '#type' => 'checkbox',
+        '#id' => 'node_pane-select_in_panels',
+        '#default_value' => !empty($settings['select_in_panels']),
+        '#description' => t('If this content type is enabled, this setting allows to select existing content inside the "Content" category of the pane selection dialog box using the view defined below.'),
+        '#states' => array(
+          'visible' => array(
+            '#node_pane-use_in_panels' => array('checked' => TRUE),
+          ),
+        ),
+      );
+
+      $form['node_pane']['select_in_panels_view'] = array(
+        '#title' => t('Select existing content in panels using this view'),
+        '#type' => 'select',
+        '#id' => 'node_pane-select_in_panels_view',
+        '#default_value' => $settings['select_in_panels_view'],
+        '#options' => views_get_views_as_options(),
+        '#description' => t('Select existing content in panels using this view.'),
+        '#states' => array(
+          'visible' => array(
+            '#node_pane-use_in_panels' => array('checked' => TRUE),
+            '#node_pane-select_in_panels' => array('checked' => TRUE),
+          ),
+        ),
+      );
+      $form['node_pane']['create_in_panels'] = array(
+        '#title' => t('Create new content in panels'),
+        '#type' => 'checkbox',
+        '#id' => 'node_pane-create_in_panels',
+        '#default_value' => !empty($settings['create_in_panels']),
+        '#description' => t('If this content type is enabled, this setting allows to create new content directly from inside the "Content" category of the pane selection dialog box.'),
+        '#states' => array(
+          'visible' => array(
+            '#node_pane-use_in_panels' => array('checked' => TRUE),
+          ),
+        ),
+      );
+
+      array_unshift($form['#submit'], 'node_pane_entity_default_bundle_form_submit');
+    }
+  }
+}
+
+/**
+ * Submit handler for our settings on the content type form.
+ * @param $form
+ * @param $form_state
+ */
+function node_pane_entity_default_bundle_form_submit($form, &$form_state) {
+  $values = $form_state['values']['node_pane'];
+  $bundle = $form['node_pane']['#bundle'];
+
+  variable_set('node_pane-' . $bundle . '-use_in_panels', $values['use_in_panels']);
+  variable_set('node_pane-' . $bundle . '-select_in_panels', $values['select_in_panels']);
+  variable_set('node_pane-' . $bundle . '-select_in_panels_view', $values['select_in_panels_view']);
+  variable_set('node_pane-' . $bundle . '-create_in_panels', $values['create_in_panels']);
+
+}