i.e. the bits where (→‎FM 3-24 Counterinsurgency) is linked-or-not.

This is because it's just taking the contents of the section-heading as-is, and in this page it contains a link:

headingText = surface.getModel().getDocument().data.getText(
	false,
	surface.getModel().getDocument().getDocumentNode().children[ 0 ].getRange()
).replace( /^\s*=+\s*(.*?)\s*=+\s*$/, '$1' );

...so it's not super-sophisticated.

(I actually only touched the visual parts of this, mostly bypassing the NWE aspects.)

It'd be pretty easy to have it, e.g., strip any wikitext links that wrap the entire section heading.

In T162017#3154847, @Jdforrester-WMF wrote:

I assume you mean https://de.wikipedia.org/w/index.php?title=Diskussion:James_N._Mattis&action=history?

I actually meant https://de.wikipedia.org/w/index.php?title=Wikipedia:L%C3%B6schkandidaten/3._April_2017&offset=20170403080000&limit=10&action=history, but got confused with the timestamp, but your example shows the same.

Change 346566 had a related patch set uploaded (by DLynch):
[mediawiki/extensions/VisualEditor@master] ArticleTarget: building summary in source mode, strip links from section titles

https://gerrit.wikimedia.org/r/346566

Change 346566 merged by jenkins-bot:
[mediawiki/extensions/VisualEditor@master] ArticleTarget: building summary in source mode, strip links from section titles

https://gerrit.wikimedia.org/r/346566