Inline markdown and external markdown files are both supported. Have a look at the "Book" example. Every chapter is in its own Markdown file. Most of the other examples have parts where I simply switch to markdown.

I am also a big markdown user and I have found that for writing reports all day long markdown clearly wins over Pug, in particular with tools like

https://atom.io/packages/markdown-preview-enhanced

But the day where you need to produce a super-nice report with a bit of custom layout, Pug/SCSS is awesome.