As a good unixaphile My conclusion is that it is because now you have two trees, a main database tree that has excellent ergonomics and tooling(the filesystem). and the registry tree where all the access patterns are special and different and the tooling sort of sucks.
I feel this article could make the same conclusion about the main filesystem if it wanted to. But I do note that because the main filesystem is not the redheaded stepchild tree, any problems with it tend to be fixed.
As a humorous footnote, I really appreciate the plan9 mindset, that single minded devotion to "The One True Tree" that when they wanted a web browser they said "hey the DOM is a tree structure. throw it in the filesystem" those glorious crazy bastards.