I think deep down, Bubbles had always accepted her to be the person the chassis was made for. Partially because of her history, partially as a memory to her comrades. And as she told Faye, she's always been different, she's embracing that.
Also, she kept the armor on not as physical protection, but emotional protection, so I guess she'd have felt way too vulnerable before to change into a civilian chassis. And now she is accepted the way she is, so she has no reason to change, rather keep it for being who she is.