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Just that editing Mail.php is the right place, or use hooks in your module and add custom variable sending the email.

public function hookActionEmailSendBefore($param)
{
    /* set default or if not exists */    
    $newgraph = _PS_IMG_DIR_.'n/custom-logo.jpg';

    /* change logo for specific template */
    $mailTemplates = array('order_conf', 'my_custom_template');

    $tpl_name = (string) $param['template'];
    $id_lang = (int) $param['id_lang'];
    
    /* if template in $mailTemplates */
    if (in_array($tpl_name, $mailTemplates, true)) {
        if (file_exists($newgraph)) {
            $message = new Swift_Message();
            $param['template_vars']['{newgraph}'] = $message->embed(\Swift_Image::fromPath($newgraph));
        }
    }
}