Take ulysses (mentioned in the article) for example. It has grown into a full-fledged writing and word processing application, but its being based on markdown originally has only hampered that. They've had to implement all of these clunky extensions and features in terms of markdown, and as the post states, try to hide the fact that it's all markdown to make it feel more like a classic word processor. At this point it just makes the whole experience clunky. People that just want to write markdown deal with weird extensions and frustrating syntax hiding, people that don't need to learn some minimal markdown just to use a word processor...
It's 2024. I hope companies start to realize that markdown is a fantastic solution for certain cases but it is not the only solution. Some applications really are better served by more complex, but much more expressive markup languages, especially if they are going to shield the user from it all anyways.