A bit of a teaser:

This bit of dwim-shell-command magic works nicely:

  (defun jtr/dwim-shell-command-pandoc-org-to-docx ()
    "uses pandoc to convert an org file to docx using a template docx file. The docx template file is stored in my synced notes folder"
    (interactive)
    (dwim-shell-command-on-marked-files
     "converting from org to docx"
     "pandoc -s '<<f>>' -o '<<fne>>.docx' --reference-doc ~/Sync/Notes/custom-reference.docx"
     :utils "pandoc"))