That's done throughout all Emacs addons: basically its text-modification API seems to have been constructed backwards from what's available to the user and the UI, instead of the other way around, and depends a lot on the cursor position. Even the more-or-less popular string library ‘s’ is a third-party addon. So Org pretty much went on with the common practice here.

With the volume of addon development that Emacs managed to get, it's a quite solid case of ‘worse is better, but you're now stuck with the worse for your life’.

There's org-element, if you want to parse/generate org-mode, but it's true that many packages just operate on the text.

org-element doesn't go far enough. Say I wanted to traverse my document in depth first order. Or in breadth first order. How do I do it? org-element does not let me choose.

I say this as there is another well known node based editor out there: Leo. Nonprogrammers manipulate their documents trivially with Python code in a way that's a huge pain in Org mode even for seasoned developers.