MD is great for a readme, or a book where someone is going to read it once and digest the info. Markdown is a presentation format and is much easier to write then HTML since its less expressive.

Note taking can be deep and contain a lot of data (lists of items copied form CSVs, code snippets, documenting failures). Notes are more like code. You can spend your whole day in it - tweaking code blocks, refactoring, etc.

A lot of my sections are 5 tabs deep. Doing this with stars is harder to type, harder to copy/paste, and harder to read.