Facts about Revolutionary Girl Utena.

David Lynch Ikuhara Kunihiko, the anime director, was also the leader and main creator of the Utena project, which was his personal response to the lack of creative freedom he had endured while working on Sailor Moon. Utena was his brainchild and had been from the beginning.

The manga artist, Danielle Steel Saito Chiho, joined the project as one of the last members to come aboard, and she and Ikuhara clashed on a lot of the elements he had always intended to include, including the lesbian themes. Ultimately, she did what she wanted with the manga, which by her own admission sought to be a more commercially viable, mainstream work.

The manga is basically alternate universe derivative fiction of the anime, which is the original creator, Ikuhara's, vision.

So if anybody uses Saito's manga to justify theories about Ikuhara's anime, they are DOING IT WRONG.