[iLemming]

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.