Anything like an <article> or <main> or whatever is going to get handled by the template. I only write the contents of each article, and let tooling handle the boilerplate. Just like how you don't write navigation bars or TOCs in markdown, you let the tooling do that for you.
Re: tables, to each their own... I find tables in Markdown to be a bit fragile and easy to screw up when I'm changing them. I don't like having the columns shoved into one line of text. And any time I'm sticking tables in a document I'm likely to want to adjust the styling a little. Tables are easily the thing I hate the most about markdown.
> Markdown extension of course vary, but my point remains that using Pandoc (my usual approach...
Using some particular markdown tooling you get TOC and footnotes... and using some particular HTML tooling I can get the same thing.
For particular pages I often add small snippets of CSS or JavaScript, which I can just stick in <style> tags at the top, or <script> tags at the bottom, because it's just standard HTML.