Ok, I was fairly certain there were no new theology stories in Runes, and I am far enough in my reread that I think I can confirm this.
Thre is a quick recap of the Clave's teachings of a-Jeroth, and at one point Linden remembers Foamy's story of the Unhomed Stars.
Since Linden never met a living Foamy, Covenant must have told her the story at some point in the Second Chronicles off camera.
I think a big part of the two theologies is that there are now two "real" people involved in the story beginning in the Second Chrons.
The original story, about the Creator, can therefore probably be "assigned" to Thomas Covenant. Since he is a creator of sorts himself, and burned his stories, this makes sense. He is both creation and destruction in one package. In addition, furthering this assignment, it (duology of creation/destruction; the Creator and the Despiser) appears in each of his summoning prophecies from Lord Foul. Everything fits together very well here.
The second set of stories, about the Worm and the Wurd, would therefore go along with Linden. Additionally, in her summoning prophecy in Runes, she sees herself with the Worm. And if the Creator, the beggar in the ochre robe, goes with Covenant's theology, this might be why he does not appear in the Third Chrons. And if the Despiser goes with Covenant, perhaps that is why he does not speak to Linden during those prophecies?
Covenant would destroy the world in the company or due to the manipulations of the Despiser; Linden with the Worm...
But what do the Worm and the Wurd have to do with Linden's inner psyche? Does the Worm/Wurd represent her terrible inner darkness that represent the detruction of life and the murder of her mother? Might the Earth represent how she built a life revolving around saving lives upon that sleeping inner murderous darkness? And the awakening of the Worm might be her greatest fear - that her new life will be destroyed if he sleeping destructive inner self ever wakes up?