When the student pitches the plan to me, I start by looking at the items in the boxes of the flowchart, to make sure they are all relevant and that no relevant things have been missed. So far, this is no different than looking at a bullet list in a conventional outline. But the next step is the key: if the diagram has A->B->C, for example, I propose some other ordering and ask the student why that couldn't work. And I also ask whether we actually need that B in the middle.
This directed-graph approach can help to reveal a good logical structure for the overall composition, often saving an great deal of time at a later stage, where the pieces being moved around are not just phrases or ideas, but rather paragraphs, sections, or even chapters.
Quite often, the best way to come up with a diagram of this type is to explain the goal of the written work to someone else, drawing the diagram as part of the explanation. If the listener says "I don't see how you got from that idea to the next" then the diagram might need another box.
The other hint I give to students is to keep updating this flowchart as the writing is being done, because the act of writing can so often uncover things that were not envisioned at the start.
PS. when I say "my student", I include myself, for the teacher who is not also a learner is missing an opportunity.