English and German introductions to typography mention that some words must not contain ligatures at certain points, such as

• shelfful
• Kaufleute

(illegal ligature in strong emphasis)

In LaTeX, one would either have to manually disable them with \kern0pt or \hspace{0pt}(such as shelf{\kern0pt}ful), or use microtype to disable them globally.

However, there's a LuaLaTeX package that does this automatically for an included selection of words: selnolig. According to selnolig's documentation, it has to be loaded after the babel package. Therefore, just using header-includes is not feasible, as that's located before.

Hence I suggest loading the selnolig package in case the LuaLaTeX engine is used, probably somewhere after line 341 of the LaTeX template:

--- pandoc-templates/default.latex	2020-07-15 00:28:58.124000000 +0200
+++ -	2020-07-15 00:31:00.189391730 +0200
@@ -339,6 +339,9 @@
 $endif$
 \fi
 $endif$
+\ifluatex
+  \usepackage{selnolig}
+\fi
 $if(dir)$
 \ifxetex
   % Load bidi as late as possible as it modifies e.g. graphicx