Markdown is ultimately a pre-HTML format and inherits its weaknesses. It is a display language.

Books have their own foibles; table of contents, notes, indexes etc. These really need a semantic approach.

Finally, I'm not suggesting anyone handcode it. I use a writing tool on my iPad that uses markdown as its file format. I never see the markdown, I just bold text, add headings etc. That was the idea, to keep it in the background. Hence the reason I'm aiming for simplicity.

Incidentally, most books need only ten tags, five of which are used exactly once on the title page.