Autonomy is not a problem of medical treatment, it's a fundamental principle of an ethical society.

Without autonomy, the concepts of voluntary/involuntary lose meaning, which can enable some very nasty scenarios. Exceptions to autonomy are rare and come with stringent legal duties and obligations on the responsible party. Doctors are not responsible for their patients in that way; they are service providers.

Lack of understanding should not be sufficient to undercut an ethical principle like autonomy. Imagine if I had the power to decide that you don't sufficiently understand the concept of autonomy, and must be shipped off to a re-education center.