Перед строкой:
$this->{'model_extension_total_' . $result['code']}->getTotal($total_data);
можно добавить примерно такой костыль:
if ($result['code'] =='total' && $total_data['total'] < 5000) {
$this->session->data['shipping_method'] = array(
'code' => 'flat',
'title' => 'Доставка',
'quote' => '100 грн',
'cost' => '100',
'sort_order' => 1,
'error' => ''
);
$total_data['totals'][] = array(
'code' => 'shipping',
'title' => $this->session->data['shipping_method']['title'],
'value' => $this->session->data['shipping_method']['cost'],
'sort_order' => 8
);
$total_data['total'] += $this->session->data['shipping_method']['cost'];
}