Conditional display of paragraphs items
So, I fixed this by writing a new module that creates custom panels panes.

Using the base Panels plugin code seen here http://fourword.fourkitchens.com/article/creating-custom-panels-panes-and-use-substitution-too I created a custom panels pane.

With the custom panels pane, I added a setting for bundles;

$bundles = paragraphs_bundle_load();
$options = array();
foreach ($bundles as $key =&gt; $data) {
  $options[$key] = $data-&gt;name;
}

$form['display_bundles'] = array(
  '#type' =&gt; 'checkboxes',
  '#options' =&gt; $options,
  '#default_value' =&gt; $conf['display_bundles'],
  '#title' =&gt; t('What bundles should be displayed?'),
);


So when adding a pane in Panelizer, there is a setting for selecting which paragraph bundles are displayed.

Then, when rendering the pane, I check which bundles are allowed and then render them, returning an html block.

$nid = $args[0];
$node = $contexts['panelizer']-&gt;data;

if ($node-&gt;type == 'article') {

  $para_ids = $node-&gt;field_nova_section_main[LANGUAGE_NONE];
  $para_ids_array = array();
  foreach ($para_ids as $delta =&gt; $data) {
    $para_ids_array[] = $data['value'];
  }

  $return = '';
  $paras = paragraphs_item_load_multiple($para_ids_array);
  $idx = 0;
  $keys = array();
  foreach ($paras as $entity_id =&gt; $entity_data) {
    if ($conf['display_bundles'][$entity_data-&gt;bundle] !== 0) {
      $return .= render(field_view_value('node', $node, 'field_nova_section_main', $node-&gt;field_nova_section_main[LANGUAGE_NONE][$idx++]));
    }
    $idx++;
  }
}

$block = new stdClass();
$block-&gt;title = '';
$block-&gt;content = $return;

return $block;


So now, rather than adding the node field to a Panelized layout, I add my custom pane and select which bundles I display.