It’s not often that the standout star of a show is its music supervisor, arranger or orchestrator, but in the gala presentation of “Pal Joey” at New York City Center through Sunday, all three are one man, Daryl Waters. More than the authors of the ambitious, bewildering revival’s new book, Waters, who has served similar roles on musicals as varied as “Bring in ’Da Noise, Bring in ’Da Funk,” “After Midnight,” “The Cher Show” and “New York, New York,” makes a clear case in beautiful sound for its investigation into…