By me, no changes of the sort you're asking about since I posted the original node
and not sure what you're seeing. Also, no auto-generation of the TOC used -- about which, see my linked response -- as edited upon posting of the "Draft...." -- to the original LanX suggestion.
In the table of contents, the entries are listed as "Basics: Para & Code markup", "Additional Markup (Overview+Examples)", and the like. In the body of the document, those same are "<h3>Chapter 1</h3>" and "<h3>Chapter 2</h3>". As LanX put it, " why not simply <h3>Chapter 1 - Basics: Para & Code markup</h3> for both?".
It had been a while since I'd read the original Markup in the Monastery node, and I had assumed that something had been changed, because I didn't remember those sections being called "Chapter 1" and "Chapter 2" in the original... but apparently I was wrong. Sorry.
I guess now my suggestion (to echo LanX), would be to use the same meaningful names that you manually chose for the TOC as the actual headers in the flow of the document. (Clicking on "Basics: Para & Code markup" and arriving at "Chapter 1" is confusing to me, and would likely confuse someone new to the document as well.)