One thing he doesn't talk a whole lot about there is sound design, I assume that's one area where episode directors would be pretty involved in.
Most shows have a "sound director" credit and the such. The usage of the soundtrack in a given episode is probably decided between the storyboarder and the episode director, with oversight by the series director as always. The article mentions how Toei tacitly expected (expects?) their episode directors to manage the voice recordings themselves, which is unusual in other studios.