Org-mode does have certain fragmentation - every Emacs config for Org-mode is different from another - there are entire packages built on top (and they drastically can change the behavior of entire system) - Org-Roam, Howm, Denote, Org-supertag, etc. Also, for what it is made for, Org-mode is widely successful - there's really not a single contender that can be used alternatively, there's literally no good replacement for it.
Comparing Markdown and Org-mode really makes no sense - different ideas, with different design goals, use cases and applications.
One of the arguments of the article is that there is a fundamental difference: Markdown was created as a small subset of syntax elements. Therefore, there was a high demand on syntax extensions that were added in a chaotic fashion.
Orgdown already comes with more syntax elements that Markdown probably will ever get. So I do see a clear argument for the case that "unstandardized additions" to orgdown are less likely in addition to the fact that there aren't any.