For extending footnotes over two columns, https://tex.stackexchange.com/questions/462347/how-to-force-a-footnote-to-extend-over-both-columns-in-a-twocolumn-article?noredirect=1&lq=1 recommends \usepackage{multicol} instead of the twocolumn document option.
Although this works for pure LaTeX documents, it will not work for generating PDF output by RMarkdown and pandoc when having Markdown-formatted elements within the multicol environment as in:
---
title: Sample Document
header-includes: \usepackage{multicol}
output: pdf_document
---
\begin{multicols}{2}
# First section
\end{multicols}
What could be a possibility to achieve footnotes extending over two columns when using RMarkdown?
Surround the \begin and \end commands with blank lines. If that doesn't work, then mark them as LaTeX snippets like so:
```{=latex}
\begin{multicols}{2}
```
# First section
```{=latex}
\end{multicols}
```