In AppleScript, how do I get the back link from an annotation document to the original?

Depends on how one goes about it, but for most normal ways that people would include custom CSS, you’re right. However, in DEVONthink 3.9.4, if you enable Prism support (in Preferences ▹ Files ▹ Markdown), the output of source of foo contains inline JavaScript code. Inspecting the output of source of foo on a simple markdown document shows the following near the top – this is just the start of the Prism part:

<style><!--
/* PrismJS 1.29.0
https://prismjs.com/download.html#themes=prism&languages=markup+css+clike+javascript+applescript+awk+bash+c+csharp+cpp+go+java+json+json5+jsonp+lisp+markup-templating+objectivec+perl+php+python+ruby+rust+sql+swift+typescript+yaml&plugins=line-numbers+highlight-keywords */
code[class*=language-],pre[class*=language-]{color:#000;background:0 0;text-shadow:0 1px #fff;fon .....

(Truncated here to save space.)

I wrote MathJax in my previous comment, but I see now that what I saw was the Prism code, not the MathJax code.