$PAGE->requires->js(); uses a path relative to $CFG->dirroot to build the path to the script.

If an admin sets $CFG->themedir and a theme in that directory has a javascript file that is called with $PAGE->requires->js() it will return an error that the file cannot be found.

to test the issue do the following:

#) set $CFG->themedir in config.php
#) add a theme to the directory set in $CFG->themedir
#) add a javascript called theme.js to the /javascript/ directory in your theme
#) add the code below to your theme to:

if (!empty($CFG->themedir)) {

    $themedir = $CFG->themedir;

} else {

    $themedir = $CFG->dirroot . '/theme';

}

if (file_exists($themedir . '/' . current_theme() . '/javascript/respond.js')) {

    $PAGE->requires->js($themedir . '/' . current_theme() . '/javascript/theme.js');

}

Result:

Coding error detected, it must be fixed by a programmer: Attempt to require a JavaScript file that does not exist.

Expected Result:
The file will be found (as proven by file_exists() returning true above) and included.