I use the system to write documents that I convert to PDF (through LaTeX), Word, plain text, and HTML, with equations, tables, and internal and external links preserved (citations in plain text turn into footnotes). It works brilliantly, and this would be impossible when starting with LaTeX source. You can embed the target formats directly into the markdown when needed, and have alternative versions for different targets. I do this for things like tables, where I want to directly format them for LaTeX and HTML, rather than rely on Pandoc’s automatic translation. You can write filters¹ that extend Pandoc/markdown to do any processing that you want, so you can create your own syntax with custom translations to any target format.
[1] https://lee-phillips.org/panflute-gnuplot/ [This is sort of obsolete now, as you should probably write filters with Lua. But it’s still a good illustration of the possibilities.]