Markdown + pandoc means it goes through an intermediary latex template on the way to pdf land - which means your markdown can be a bastardized mix of markdown, html, latex commands, and sometimes more ;)

This is just basic make changes to file, git add and commit workflow. Other features of git like branching can be leveraged for greater control but are optional. What makes it magical is 3 seperate systems working together with such symphony namely git, Zotero and pandoc. Zotero is citation manager that you can use store scientific articles, papers, thesis etc. and it can produce a bibliography file and pandoc can reference those along with the citations in the make file to create a clean typesetted Word or LaTeX pdf with precise numbering, table of contents, citations and bibliography with correct format without you needing to edit anything.

I absolutely love R markdown! Being able to iterate on your analysis and report at the same time is fantastic