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Pandoc defines the variables for the template and we use them:
https://pandoc.org/MANUAL.html#variables-for-latex

It seems there is a indent parameter that can be set to true to avoid default Pandoc adjustment
https://github.com/jgm/pandoc/blob/main/data/templates/default.latex#L204-L216
and we use the same

$if(indent)$
$else$
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
\KOMAop…

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@eteitelbaum
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@cscheid
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