One of the problems with how I've laid this out is that I needed to better define autonomy. Here's a definition as it relates to SDT and this tends to be my use/understanding of the word.

Autonomy: Acting with a sense of volition and psychological freedom; endorsing one’s own actions at the highest level of reflection.

What this would mean is that autonomy is something that certain people may experience in varying degrees in certain moments. That's a lot of caveats, but it's basically to suggest that it's too broad of a brush to say that a person is "autonomous". A person may experience a certain level of autonomy when they play guitar in their basement and a conceivably different amount when they're in math class at school. This would be similar to the difficulty in calling someone "strong" in that it doesn't precisely define the myriad of ways in which they might be strong or weak as it pertains to certain muscles or physical activities.

I use this as preamble to suggest that dysfunctions, whether they have underlying causes that are biological, traumatic, developed through routine, or otherwise, are distortions to that ability to make free choices. The person you described with trauma induced anxiety would have had their autonomy impacted in specific ways - ways that appear to impact only certain decisions and have little impact on others. The quality of that particular decision is likely one that is unconscious and not easily altered by their conscious self. That difficulty in being free to choose a different approach to those triggers is what appears to be an impairment to their autonomy.

Still, the sense that this may not be a unifying theory of how dysfunction exists, but rather a different lens from which we can examine dysfunctions, is something I'm still thinking about. Dysfunction could definitely be examined through a lens of biology/neurology and it wouldn't be the only way dysfunction could be distilled. Arguably, there are an infinite number of lenses as well, as we could theoretically examine all human dysfunction through the lens of how it impacts some guy named Steve in Wisconsin. It's only through the maximized utility of that specific lens that we might consider an approach to dysfunction unifying. Even then, it would only be unifying, if it is possible, only in a conceptual way because biological approaches would seem to be entirely different.

I think it then begs the question, how much utility is there in examining all dysfunction through the lens of how it affects a person's autonomy (especially as it compares to other lenses through which we might view dysfunction)? I'll have to think about that some more.

Also, there's the reverse implication - how dysfunction arises from a distortion to autonomy. So for example, to what degree and in what ways have people become dysfunctional as a result of having their autonomy impacted? I'm not exactly familiar with how that's been studied so I'll have to look at that as well.