Preserve normal Drupal messages on checkout pages

As a follow-up to #1212482-30: hook_commerce_payment_order_paid_in_full() does not fire in module hook, we've had a long standing issue regarding site messages on checkout pages (even on the completion page which is still built through the normal checkout form builder). We do a sort of early detection looking for error messages so we can display them inline with the particular checkout pane that failed, but it appears that normal messages are not being "put back" to appear properly. In fact, I tried to debug this for the last half hour and got nowhere... I believe the expected behavior is only:

1) Error messages from any given checkout pane should be displayed right above that pane (as opposed to at the top of the page with any other errors).

2) Other messages, including status messages, should be preserved.

I believe the issue is with the monkey'ing with $_SESSION['message'] in `function commerce_checkout_form_submit($form, &$form_state);` in modules/checkout/includes/commerce_checkout.pages.inc

function commerce_checkout_form_submit($form, &$form_state) {
  global $user; 

  $checkout_page = $form_state['checkout_page'];                                                                

  // Load a fresh copy of the order stored in the form.
  $order = commerce_order_load($form_state['order']->order_id);

  // Catch and clear already pushed messages.
  $previous_messages = drupal_get_messages();

  // Loop through the enabled checkout panes for the current page.
  $form_validate = TRUE;
  foreach (commerce_checkout_panes(array('enabled' => TRUE, 'page' => $checkout_page['page_id'])) as $pane_id => $checkout_pane) {
    $validate = TRUE;

    // If the pane has defined a checkout form validate handler...
    if ($callback = commerce_checkout_pane_callback($checkout_pane, 'checkout_form_validate')) {
      // Give it a chance to process the submitted data.
      $validate = $callback($form, $form_state, $checkout_pane, $order); 
    }

   // Catch and clear panes' messages.
   $pane_messages = drupal_get_messages(); 

    // Submit the pane if it validated. 
    if ($validate && $callback = commerce_checkout_pane_callback($checkout_pane, 'checkout_form_submit')) {
      $callback($form, $form_state, $checkout_pane, $order);
    }
    // Generate status messages and theme them.
    $_SESSION['messages'] = array_merge_recursive($pane_messages, drupal_get_messages());
    $form_state['storage']['messages'][$pane_id] = theme('status_messages'); 

    // A failed pane makes the form fail. 
    $form_validate &= $validate;
  }

  // Restore messages and form errors.
  $_SESSION['messages'] = $previous_messages;
  ...
}