These are good points, but are mostly pragmatic, resulting from the rest of the system not being designed around a tree representation. Of course, that can be decisive in practice...

A more fundamental issue (which I mention in the document) is that there is a discordance between the 2D textual display and the underlying tree. I think this becomes more apparent when input is not only keystrokes, but also mouse positioning.

Of course, these disadvantages do not necessarily outweigh the advantages of editing in terms of trees!