Basically you can try this following code, add into that email template php file.
<?php
$db = ES::db();
$query = 'SELECT `id` FROM ' . $db->nameQuote('#__users') . ' WHERE `username` = ' . $db->Quote($username);
$db->setQuery($query);
// Retrieve the user id which registered on the site
$userId = $db->loadResult();
$userData = ES::user($userId);
// set your CUSTOM FIELD UNIQUE KEY
$uniqueKey = '';
$customFieldValue = $userData->getFieldValue($uniqueKey);
?>
<?php if ($customFieldValue) { ?>
<tr>
<td style="padding: 5px 0;">
<?php echo JText::_( 'Extra Info' ); ?>: <?php echo $customFieldValue;?>
</td>
</tr>
<?php } ?>
Check your custom field unique key from backend
http://take.ms/w1iJ4 , then put this key into above code
$uniqueKey = '';
e.g. $uniqueKey = 'school-start';
It also depend on what kind of custom field you want to retrieve, different custom field have to use different code.
For this example is, I use the textbox custom field.