Yes, the markup is hidden and the document is rendered in all cases. The point I was making, and I believe the parent was making, is that it doesn't have to be wed to the physical medium. Perhaps we're talking past each other here.
Writing markdown is decidedly not WYSIWIG. Storing documents with a WYSIWIG editor in a markdown-like format isn't viable either - look how frustrated word processor users get if changing one element repositions another ("all my pictures move"). Users want things in a precise format.
Nobody is proposing that people will be writing markdown by hand in text editors. Just that a lot of the complexity of rendering stuff on the screen precisely as it would be printed on, say, A4 paper can perhaps soon be left behind. People print a lot less these days, and thus WYSIWYG (in the original 70s, 80s and early 90s sense of the term https://en.wikipedia.org/wiki/WYSIWYG) may be less important.
