I'm not sure that's quite right, though I may have misunderstood something.
On pages 53-60 of CBT for Adult Asperger Syndrome, Gaus discusses core cognitive and processing deficits in autistic people. She discusses emotion perception and regulation, alexithymia, sensory-motor processing, dysfunctional processing of information in nonsocial domains, flexibility, planning, and central coherence.
Her conclusion is
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The core cognitive dysfunction described above causes individuals with AS to engage in a multiude of maladaptive behaviors that lead to negative consequences for them, further compound their problems, and cause emotional distress. When one of these adults presents for psychotherapy, it is rare that he or she seeks help with an isolated core AS problem, as illustrated by the seven cases described in chapter 1. Usually the patient's AS symptoms have become interwoven in a complex web of environmental stressors and comorbid mental health problems, and this web leads the therapist to a broader conceptualization of the individuals presenting problems.
And when discussing more traditional behaviorist models (Beck's cognitive model) she doesn't dismiss the real roots of negative schemas:
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The cognitive model assumes that fellow human beings are a great source of teaching, modeling, and reinforcing the beliefs that comprise schemas. However, social cognition deficits make it much harder for persons with AS to infer and make use of information that comes from other people in a social context. They therefore miss out on a rich source of input for developing and evolving healthy schemas appropriately over time. Their cognitive inflexibility is also a risk facto in that they may hold on too strongly to a schema that is nonfunctional. Their frequent experiences of negative life events, such as social rejection and repeated employment failures, are likely to reinforce negative beliefs about self, others, the world and the future.
While she does see these as contributing to anxiety and depression, she isn't saying the maladaptive schemas are not based in reality. And while she does see all of these as potentially contributing to anxiety and depression, I don't see an argument against any other cause for either. On the contrary, on page 87, she mentions GAD and Major depression as biologically rooted in people with ASDs:
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Again, the arousal symptoms are difficult to assess in these patients who are so prone to regulation problems. Nevertheless, does the patient's persisitent worries seem to be linked to restlessness, fatigue, difficulty concentrating, irritability, muscle tension, or sleep problems?
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As described in chapter 2, adults with AS are predisposed to mood disorders from genetic, neurobiological, and psychosocial perspectives. Once the diagnosis of AS or HFA has been established, the therapist should assume high risk for mood symptoms...
It seemed to me when I read it the first time that she both acknowledges that innate factor and tries to work with awareness of it but thinks the tools of CBT can help to deal with maladaptive schemas layered on top of the core AS features.
Certainly, I think about this when I hear my son say. "I suck at life," as he struggles with homework, and I recognize how much he is like me both in his overwrought emotional response and the executive functioning issues that turn simple but boring work into a huge, grinding chore. I don't see the CBT approach helping with the EF stuff, but if they can put the lie to the inner message, "I suck at life," that would be a good thing.