Pear mail for SMTP does not use the mail() function to send the email.
In the PEAR_Mail_using_SMTP_PHP.php file, the lne that sends the email is:
$mailObj = $theMailer->send(str_replace(";", ",", $mailTo),$headerArray,$mailBody);
If you where to use the Mail email object, that Does use the mail function. The line that sends the email in the mail_PHP.php file is:
$mailObj = mail($mailTo,$mailSubject,$mailContent,$mailHeader);
The only two mail objects we support are mail or Pear mail for smtp. The pear mail for SMTP uses the onlly alternative mail function we offer.