The 5th reason especially You can convert markdown into other formats such as PDF, Word, Media WIKI etc using pandoc (I am sure there are other programs). It is trivial to write a shell script or similar to convert markdown files into another format.
> After that, it is hard to migrate to another tool, as custom-defined HTML classes and flavor's features won't work outside the current set of tools and page designs.
That contradicts his Lack of Extensibility. Typically anything custom you do outside what is supported officially by the tools maintainer is your own lookout.
Markdown is a like a lot of things that succeed. It is good enough to produce well formatted documentation to be read by a client and simple enough for people to learn it relatively quickly without headaches.