My wife is an author and I handle all of the digital/print book creation. After 4+ years of using various tools I decided to streamline my process.
It can be a pain to manually update a Bio page with new information or new books for example. Doing a simple thing like that for 3 formats of a dozen books can take time and introduces the possibility of new typos with every change.
Pandoc is a great tool to convert markdown files to html/epub/pdf etc. but it's epub templating is still very minimalistic. It requires multiple stages to create a template that allows me to reuse common pages such as biography, licensing, etc.
I love Jekyll and use it whenever I can for web design. One of my favorite aspects is the ability to define 'code chunks' in the _includes folder and then use reference it wherever I want. Change that include file, rebuild, and every reference to it on your website is updated. It's that kind of logic that I need for creating my books.
By using Jekyll's templating I'm able to create files that slightly differ based on need. The mandatory Smashwords title page for example, or a custom Title page with Amazon URLs to other books.
Jekyll allows me to create custom templates, multiple 'includes', and then outputs them in a perfectly formatted Markdown file.
This markdown file can then be passed along to Pandoc and converted to epub/mobi/pdf.