A prison does not only lock its inmates inside, it keeps all others out. Her strongest prison is of her own construction.
In this first quotation, Dr. Jordan realizes that Grace is withholding information. He says that Grace has, metaphorically, created her own prison, which keeps him out but which also keeps her in. Ironically, however, it is this mental prison of Grace's own construction, which protects her. It is one of the few ways in which she can claim her own inviolate space, into which the various male authority figures in her life can not intrude.
I was there in the box of the dock but I might as well have been made of clot, and stuffed, with a china head; and I was shut up inside that doll of myself, and my true voice could not get out.
In this second quotation, Grace is describing her trial. She says that she feels metaphorically, "shut up inside that doll of myself" so that her "true voice (can) not get out." In other words, she feels constrained by the rigid social perceptions of her. Her guilt is predetermined and whatever voice others hear is only the voice that they want to hear and insist on hearing. Grace's true voice is muffled behind the "doll," which is a metaphor for the artificial, dehumanizing female construct that is, in the story, imposed upon all women.
When you are in the middle of a story it isn’t a story at all, but only a confusion; a dark roaring, a blindness, a wreckage of shattered glass and splintered wood.
In this third quotation, Atwood implies that a story is a linear narrative that we retrospectively fit to a sequence of events that otherwise, independently, have no inherent meaning. When we experience these events, in the moment they are chaotic, "a wreckage of shattered glass and splintered wood." We only later try to fit them into a story to attribute meaning to them. Another way of looking at this is that no independent events can be understood until they are put into a wider context, which is what a story provides.
The metaphors that Atwood employs in this excellent novel frequently have the purpose of elaborating on the curious position that Grace Marks finds herself in as she is the topic of massive discussion and debate. As Atwood assumes the voice of Grace, the wry humour and slightly sardonic approach to what is happening around her can be detected in the metaphors she uses in addition to the horror of her situation, as in the following example when she is starring at the flowers in the Turkey carpet in Chapter 3:
They have petals the shape of diamonds on a playing card; like the cards spread out on the table at Mr. Kinnear's, after the gentlemen had been playing the night before. Hard and angular. But read, a deep thick red. Thick strangled tongues.
There is both a horror in this metaphor where the supposed petals are compared to "thick strangled tongues," which indicates the horror of Grace and what she has experienced and undergone. But there is also an ironic reference to the petals as "strangled tongues." Grace relates the petals to the diamonds on playing cards, the leisure activity of men, and it is the male doctors who do their best to classify her and tell her what is wrong with her, and therefore the use of this metaphor could also refer to their botched attempts to treat her as a medical curiosity and "diagnose" what is supposedly "wrong" with her.