Linux

Markdown, CommonMark, .rst formats are good for printing basic rich text for technical documentation and so on, when text styling is made by an external application and you don't care about reproducible layout.

But you also want to make custom styles (font size, text alignment, colours), page layout (paper format, margin size, etc.) and make sure your document is reproducible across multiple processing applications, that the layout doesn't break, authoring tools, maybe even some version control, etc. This is when it strikes you bad.

Markdown misses checkboxes anywhere, especially in tables.

But markdown is just good. It's just writing text as normal basically

You can convert Markdown to a number of formats with pandoc, if you want to author in Markdown and just distribute in some other format.

Not going to work if you need to collaborate with other people, though.