About this, I misunderstood as you did not shared what results you had. I though the & was converted to something else.
I believe the & is escaped as it is seen as raw Markdown, then converted to LaTeX and I believe & in LaTeX needs to be escaped, unless in table environment maybe ?
It seems Pandoc will at least escape it because not in a LaTeX block. Pandoc is doing the conversion from & to \&. If you use raw LaTeX in the markdown though, it will keep it as is
\begin{tabularx}{\linewidth}{p{0.5\linewidth} X}
\toprule
Column 1 & Column 2 \\
\midrule
\textbf{Lorem} & Ipsum \\
\bottomrule
\end{tabularx}
without escaping.
As I said, it is a limitation of Pandoc : Markdown syntax can't be mixed within a LaTeX block.
This would be interesting to share what you are looking for. R offers a lot of table framework and it would be interesting for them to know that you have a use case not handled by them.
I don't know what is missing really from what you described, but maybe there is a way you did not find. kable() can take table.envir argument among other to customise the LaTeX written. xtable has a tabular.envir and example in its doc with tabularx.
I am sorry I can't help more. I believe you are encountering the limitation mentioned above. If you can't use a R package for that, you need to write Markdown Table or Raw LaTeX directly in a way that Pandoc can convert them correctly.