I managed to sneak my analytics JS code into the end of the Custom CSS box by ending the </style>
tag, adding the JS and then opening another <style>
tag.
e.g.
/* custom CSS */
</style>
<!-- Fathom - simple website analytics - https://github.com/usefathom/fathom -->
<script>
(function(f, a, t, h, o, m){
a[h]=a[h]||function(){
(a[h].q=a[h].q||[]).push(arguments)
};
o=f.createElement('script'),
m=f.getElementsByTagName('script')[0];
o.async=1; o.src=t; o.id='fathom-script';
m.parentNode.insertBefore(o,m)
})(document, window, '//fathom.domain.com/tracker.js', 'fathom');
fathom('set', 'siteId', 'ABCDE');
fathom('trackPageview');
</script>
<!-- / Fathom -->
<style type="text/css">
/* closed by the code which injects the custom CSS */