Hugo wasn't including header elements generated with the tag-def-box into the table of contents. This is a known problem with Hugo. I am using jakewiesler's work-around where you use Markdown headers in the short code and call it with {{% short-code %}} instead of {{< short-code>}}. This also makes the generated headers consistent with the rest of the headers in the document.

This does lose the ids which were the .ass code rather than plain-language description.