The game's final boss, Toyosatomimi no Miko, is based on the legends of Prince Shoutoku, a political figure who lived during the Asuka period in Japan. Most notably, Miko shares the exact same birthday, is stated in supplementary materials to have lived in the world outside Gensokyo, and even shares the ability to understand ten conversations at once.

Miko's identity as Prince Shoutoku is also referenced in the name of her leitmotif, "Shoutoku Legend ~ True Administrator."

Most stages/bosses in the game actually have two slightly different themes. When a playable character enters Trance Mode, the music will shift to a "Spirit World" version. The normal stage themes have more of a focus on the melody and harmony of each track, while the Spirit versions have a lower sampling rate and focus much more on the rhythm. The two versions can also be mixed for a more "full" version.

It is possible that Toyosatomimi no Miko's theme lacks a Spirit World version. It is thought that this ties into Miko's ability to listen to peoples' desires, regardless of whether they are a spirit or not.