Character charts are not the same as plotting blow by blow accounts on every chapter. I write on a yellow pad to keep track of my characters and do an occasional flow chart to make sure the plot stays consistent.
He also uses flow charts. Nothing wrong with using them. As you point out it helps with consistency of plot development. Charts don't need to be "blow by blow," merely an outline that best suits the author's needs. Whatever the craft, we all need tools. For a writer a chart can be a valuable tool. Should the writer transcend from craft to art, the tools did their job.
Critics claimed James Joyce's "stream of consciousness" was natural writing at its peak. However, Joyce was the ultimate meticulous craftsman who carefully planned out and then analyzed every sentence he wrote, rewriting often to achieve his goal, the appearance of "stream of consciousness." Joyce understood, as expressed in some of his letters, we "do not always think with words, sometimes with recalled sounds, at times with images."
A fellow I know swears by natural writing. He makes his living writing film and TV scripts. Toward the end of each work session, he goes back and charts out his progress, then makes corrections as the charts dictate. Whatever methodology works for each of us is good.
I am a very structured guitarist, thinking carefully about scales, keys, progressions, and so forth. Occasionally, I reach those moments when I stop thinking about what must come next and just play. I see the difference when I glance at the faces of the audience. The structure was still there, but sublimated to the making of music. Perhaps, moments of art?
Charles Mingus would wander the streets, unbathed, unshaved, in his pajamas and a robe, for days. People thought he was drunk or on drugs. He wasn't. With the concern of his loving wife, during a court ordered psychiatric evaluation, Mingus told a psychiatrist, "the music plagues my mind, I follow the music." The psychiatrist ruled that Charlie wasn't insane, nor a substance abuser, he was a genius who thought differently than the rest of us and was composing as he wandered. He was no danger to anyone, or himself. Thereafter police, when they picked up Charlie in the street, would drive him home to his wife, instead of the local precincts to dry out.