For non SMTP e-mails sent, if you add the line $mail->setMessageId(); before @$mail->send(); it will send an e-mail with piwik url in Message-Id e-mail header.
eg:
// send email with new password
$mail = new Mail();
$mail->addTo($email, $login);
$mail->setSubject(Piwik::translate('Login_MailTopicPasswordChange'));
$bodyText = str_replace(
'\n',
"\n",
sprintf(Piwik::translate('Login_MailPasswordChangeBody'), $login, $ip, $url)
) . "\n";
$mail->setBodyText($bodyText);
$mail->setFrom($this->emailFromAddress, $this->emailFromName);
$replytoEmailName = Config::getInstance()->General['login_password_recovery_replyto_email_name'];
$replytoEmailAddress = Config::getInstance()->General['login_password_recovery_replyto_email_address'];
$mail->setReplyTo($replytoEmailAddress, $replytoEmailName);
$mail->setMessageId();
@$mail->send();
Message-Id will be shown
Message-Id: < ...@piwik.url.com >
instead
Message-Id: < ...@server.com >
It will be useful for severs sharing several piwik installations.