So if it makes a one line change to Load.php - and not index.template.php, it must be doing something else internally to be able to serve the JS (which is not quite a hook but a global variable)
Here is the entire Install.xml:
<?xml version="1.0"?>
<!DOCTYPE modification SYSTEM "http://www.simplemachines.org/xml/modification">
<modification xmlns="http://www.simplemachines.org/xml/modification" xmlns:smf="http://www.simplemachines.org/">
<id>TapatalkSMFPlugin:TapatalkDevelopmentTeam</id>
<file name="$sourcedir/Load.php">
<operation>
<search position="after"><![CDATA[ $context['menu_separator'] = !empty($settings['use_image_buttons']) ? ' ' : ' | ';]]></search>
<add><![CDATA[ $context['html_headers'] .= '<script type="text/javascript" language="JavaScript" src="' . $boardurl . '/mobiquo/tapatalkdetect.js"></script>';
]]></add>
</operation>
</file>
</modification>
Everything else, including replacements for many key SMF source files, is contained in the Mobiquo directory.
I removed it because none of my members were using it, those that access with a handheld device prefer the "Mobile Curve" theme.