The author appears to have some recency bias that misses the point of Markdown. It didn't start when it was named and mapped to HTML. It was in use on usenet and in emails before HTML even existed. And most of its conventions came from typewriters before that.
You could print out a Markdown document today and jump in a time machine to 1970 and hand it to someone and they'd understand it. Chances are they still will in 2070.
In the meantime we've had countless proprietary binary word processor formats that couldn't be read before their program was released and most of which can't be read today. We've had bad attempts to replicate print publishing designs and unusable Flash websites. We've had a variety of markup formats including HTML, XML, etc. which are relatively a pain to read or write. We've had lousy WYSIWYG editors that never work correctly. And we've stored the documents split into chunks in databases. And now the suggestion is to write text as JSON data structures?
All that stuff has its place, but none of it has the timelessness and clarity of plain text and markdown when it comes to documents.
It's not particularly good for structured data. Nor multimedia (though you can reference it with links). But it's still quite good at what it is good at. Has been since before HTML and will be long into the future.