Seems like the best solution is to just edit the default template and call it with the pandoc --template option. As described at https://superuser.com/questions/356032/markdown-to-latex-conversion-with-a-custom-preamble-using-pandoc .
When converting from Jupyter to LaTex, the Latex output includes \usepackage{xcolor}. How to have it include \usepackage[table]{xcolor}? (The [table] option is required for use with Jupyter/R's knitr functionality.)