Not sure of the relevance of issue 2956, which is about pandoc not recognising options in parentheses. There are no parentheses in the problematic header inclusion.

On Tuesday, 8 August 2017 03:56:00 UTC+9:30, John MacFarlane wrote:

See https://github.com/jgm/pandoc/issues/2956

Alternatively, in the dev version of pandoc you can tell
it you've got raw latex, not Markdown:

header-includes:
- `\let\oldsection\section`{=latex}

Final remark:  I don't understand why it's not parsing
the `\section` as raw tex.  I'll need to look into this;
it may be a bug in the LaTeX reader.

+++ David Nebauer [Aug 07 17 00:39 ]:
>   If I process this markdown file ('mwe-latex.md'):
>   ---
>   title: "Minimal Working Example"
>   header-includes:
>   - \let\oldsection\section
>   - \renewcommand{\section}[1]{\clearpage\oldsection{#1}}
>   ---
>   Text.
>   with the pandoc command:
>   pandoc -t latex --latex-engine=xelatex --output=mwe-latex.pdf
>   mwe-latex.md
>   I get the the error:
>   ! LaTeX Error: Missing \begin{document}.
>   See the LaTeX manual or LaTeX Companion for explanation.
>   Type H <return> for immediate help.
>   ...
>   l.49 \let\oldsection\textbackslash{}s
>   pandoc: Error producing PDF
>   On generating latex output with the command:
>   pandoc -t latex --latex-engine=xelatex --standalone
>   --output=mwe-latex.tex mwe-latex.md
>   and examining line 49 of the output file it becomes apparent that this
>   line from the header inclusion:
>   \let\oldsection\section
>   has been munged by pandoc to:
>   \let\oldsection\textbackslash{}section
>   and this is causing the processing problem. (Note: changing latex
>   engines makes no difference.)
>   Once line 49 is edited to resemble the original command from the header
>   inclusion the error disappears.
>   How can I prevent this latex command in the header inclusion from being
>   munged by pandoc?
>
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