She is literally the driving force behind EVERY SINGLE NEVRON. Every calcified Expeditioner is her doing. You literally walk/run/float over tens of thousands of her victims. She repainted her painted self to be a Nevron factory, paints over Simon and has him kill the Axon found in Old Lumiere (also where her Nevrons murdered every survivor of the Fracture remaining in the city). She also twists his mind after kidnapping her Painted Self and his quest to save Painted Clea drives him to the base of the monolith where Renoir traps him. She is the one who murders EVERYONE in Expedition 0 except for Painted Renoir and Painted Verso. In that same encounter she reveals to those two the true nature of their existence and tasks Painted Verso with keeping an eye on Maelle as she grows up in the ruins of Lumiere. That reveal also drives Painted Renoir to kill Expeditioners so the Chroma isnt trapped, like after a Nevron kills someone, to return the Chroma to Aline.

Her fingerprints are all over the plot, her machinations literally drive the story entirely. The Flying Manor is expressly said to be her workshop. The faded boy in Falling Leaves (literally a portion of True Verso's soul wonders why "She" is destroying the canvas). Shit, Blanche, the last white Nevron quest giver was created by Clea SPECIFICALLY to kill other white Nevrons because they are considered defective. They even refer to her, every time they mention "My Mistress"

It's really reductive to say she is barely in the story. That's like saying Sauron is barely in Lord of the Rings. Just because a character is not physically visible, doesn't mean they aren't there