Alter Fieldable Panels Pane form
Almost all Drupal forms can be edited using hook_form_alter(), specifying the form using its id:

Hide "Make title a link" for all fieldable panels panes:

/**
 * Implements hook_form_alter().
 *
 * Simplify form for fpp.
 */
function your_module_form_alter(&amp;$form, &amp;$form_state, $form_id) {

  if ($form_id == 'fieldable_panels_panes_fieldable_panels_pane_content_type_edit_form') {
    $form['link']['#access'] = FALSE;
  }
}


Hide "Make title a link" for all fieldable panels panes of the type "your_bundle":

/**
 * Implements hook_form_alter().
 *
 * Simplify form for 'your_bundle' fpp.
 */
function your_module_form_alter(&amp;$form, &amp;$form_state, $form_id) {

  if ($form_id == 'fieldable_panels_panes_fieldable_panels_pane_content_type_edit_form') {
    if ($form['#bundle'] == 'your_bundle') {
      $form['link']['#access'] = FALSE;
    }
  }
}