The emails sent out by the system are sent by the PHPMailer script, which allows you to do pretty much anything you need to do with sending emails in PHP.
The PHP code for the configuration and sending of emails is in process.php and you can find the start of it by searching for the term $mailer.
If you need to make a change to these settings you can do it there, most of the code is commented to help you make changes. You should also check out this PHPMailer tutorial to help you customise the settings.
The email is sent using PHP’s mail() function by default, if your host does not support this, you can change it to use a SMTP server instead. See the page Sending emails via an SMTP server for how to do this.