Not sure about what you want to do, because `wkhtmltopdf` is a translator from html to pdf.
Rmarkdown use `pandoc` to generate document. Anyway, you can change latex engine, if you need, but with some restrictions, you can use one of “pdflatex”, “lualatex”, “xelatex”, “tectonic”.
You can find many configuration options in External link to document configuration
Hope this helps