A <script src="…" defer> always runs with a body, which is nice in any case since it keeps scripts together, lets the browser start loading every script right away, and is explicit about which ones need to run before the body. Sadly, defer is only allowed for script elements with a src attribute.
<html>
<body></body>
<head><script>alert(document.body);</script></head>
</html>
This is why window.onload and then jQuery's document.ready, and later, putting the script at the end of your file, is a best practice.
The parser creates an empty head element when it sees the <body> start tag, the second <head> start tag is ignored, and the <script> is treated as part of the body element. Try changing the body of the <script> tag to this:
alert(document.currentScript.parentNode);
The behavior is specced out here, if you're curious: https://www.w3.org/TR/html5/syntax.html#parsing-main-afterbo...