This is pretty much exactly what I do, too. The only difference is that my use of Apple Notes is mostly for quick, personal things ... I move material into Markdown documents within git repositories as soon as I can, because then it's easy to share it, trace changes, and organize contributions.

Oh, and one more thing: my Markdown documents are normally R-Markdown documents, so I can incorporate calculations and graphs as needed. (Also, R-Markdown has a nice metadata section for document title, author, date, etc.)