Change the subtotal amount in commerce_email_order_items
Well, after re-examining the code of the commerce_email.module, I had an epiphany, and finally get it.

Here is the code before my change (starting line 169) :

$data = $wrapper-&gt;commerce_order_total-&gt;data-&gt;value();
  if (!empty($data['components'])) {

foreach ($data['components'] as $key =&gt; &amp;$component) {

  if ($data['components'][$key]['name'] == 'base_price') {
    $rows[] = array(
      'data' =&gt; array(
        ' ',
        array('data' =&gt; t('Subtotal:'), 'style' =&gt; array('font-weight: bold; text-align: right;')),
        array('data' =&gt; number_format(commerce_currency_amount_to_decimal($data['components'][$key]['price']['amount'], $currency_code), 2), 'style' =&gt; array('font-weight: bold; text-align: left;')),
      )
    );
  }


And now with my change :

$data = $wrapper-&gt;commerce_order_total-&gt;data-&gt;value();
 if (!empty($data['components'])) {
  foreach ($data['components'] as $key =&gt; &amp;$component) {
         if ($data['components'][$key]['name'] == 'flat_rate_expedition_internationale' || $data['components'][$key]['name'] == 'flat_rate_expedition_outremerre' ) {
            $amount_expedition = $data['components'][$key]['price']['amount'];
          }

  }
  foreach ($data['components'] as $key =&gt; &amp;$component) {
      if ($data['components'][$key]['name'] == 'base_price') {

          $amount_base_price = $data['components'][$key]['price']['amount'];
            if (isset($amount_expedition)) {
                $amount_base_price += $amount_expedition;
            }
          $rows[] = array(
              'data' =&gt; array(
                  ' ',
                  array('data' =&gt; t('Prix HT :'), 'style' =&gt; array('font-weight: bold; text-align: right; margin-top: 10px')),
                  array('data' =&gt; number_format(commerce_currency_amount_to_decimal($amount_base_price, $currency_code), 2), 'style' =&gt; array('font-weight: bold; text-align: right;')),
              )
          );
      }


It's not a great solution, and I will try to make a full module, to select dynamically the components to add to the base_price.
Until then, this will do the job.