Hey, I just wanted to give some belated thanks for the advice; it turned out to be key in my eventual understanding of how to encode these points! I also wanted to update this thread because I think I figured out what the source of my confusion was.
Basically, I realized recently that the MC's critical flaw of suspicion is less about her seeming suspicious to the other characters, but more about her being wary and taking sensible precautions in hiding her truth from the other characters. In short, she has good reason (based on prior evidence) to think that the other characters in the OS will never be able to understand her problem-- or that even if they do understand it, they won't accept her because of it. This prompts her to be wary of sharing too much of herself with the other characters, thereby preventing them from understanding the true nature of her problem. Thus her critical flaw is indeed the thing undercutting the achievement of the story goal by the other characters, not the thing undercutting HER achievement of her own goal/response to her problem, as I initially hypothesized.
Likewise, my interpretation of her unique ability of prediction as being "the thing that best enables her to stop the other characters from achieving the story goal," as per my original post, was incorrect. In fact, the unique ability is the thing that would enable her to realize that her efforts throughout the course of the story are in vain, and that she should stop pursuing her personal symptom of "ability" in order to pursue her true solution of "equity." If she engaged with her unique ability, she'd recognize that her destiny is unchangeable, and that the quicker she can surrender to it, the better for everyone involved. However, her wariness holds her back, to the extent that the story ends in failure. She resolves her personal angst in the end, but without enabling the characters in the overall storyline to achieve their story goal of understanding what her secret was in the first place.
I think my confusion stemmed partly from an improper understanding of Dramatica terminology, and also from the fact that my MC is very concerned with seeming suspicious to the other characters (to be expected, perhaps, as "awareness" is in fact the direction/response of the relationship throughline). She spends most of the story arguing with her IC about being/seeming suspicious to others, and thus "suspicion" made sense to me as what was holding her back from achieving her personal goal of thwarting the other characters. But that is not a sufficiently objective reading of this trait.
I think you're right that from her POV, the MC sees the unique ability and critical flaw as being reversed:
From my MC's POV, she sees her suspicion (i.e. her tendency to be wary of others for semi-justified reasons and her tendency to take sensible precautions to avoid their uncovering of the true nature of her problem) as not only important, but vital to her survival. And it is her unique ability of prediction that is the niggling doubt in the back of her mind that tells her that her problem will never go away unless she throws her waryness/suspicion out the window in order to embrace her truth, damn the consequences.
HOWEVER, this does not mean that MY view of these traits as the author of the story should be equally mixed up, because from an objective POV, her unique ability and critical flaw are exactly what they claim to be on the tin: the thing enabling her to aid the achievement of the overall story goal, and the thing that is preventing her from doing so, respectively.