I've been sleeping on best practices here... is it preferred to do a script with defer in the <head> over putting it at the bottom of the <body> now?

I'd say yes. Defer-in-<head> works just like bottom-of-<body>, except the browser can start downloading and parsing the scripts right away (and in parallel if it wants).

Doesn't matter much with defer or async. If you but the at the bottom, they start loading in parallel slightly later.

Which could be a good thing or bad thing depending on its importance to the experience.

That's just because of ordering, though. Test it:

    <html>
      <body></body>
      <head><script>alert(document.body);</script></head>
    </html>

works fine. It's not a head vs. body distinction, it's just that the parser is stopped during inline scripts, and doing e.g. getElementById won't work if the script is declared after you.

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.

What's happening isn't what you think is happening.

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);

It alerts "[object HTMLBodyElement]".

The behavior is specced out here, if you're curious: https://www.w3.org/TR/html5/syntax.html#parsing-main-afterbo...