Can you elaborate the better header structure?

Org mode supports adding metadata to the whole document (a la pandoc, frontmatter) and any node. There are a lot of properties (dates, settings, user defined ...).

With pandoc, the frontmatter metadata are only used when exporting the document. With org mode, the metadata are also used during editing, executing code, etc.

The headings themselves can embed tags.

Turns out this is me mis-remembering. They're basically identical.

Probably it's just org-mode's useful built-in shortcuts for moving the headers around and folding them that made me think it was better in that regard.

Presumably there are markdown editors with similar behaviour.