Right, that's the problem. The fact that doctors must ask for the consent of people who don't understand what they are consenting to.
The idea itself isn't that controversial - age of majority laws for contracts, voting, and even medical treatment clearly acknowledge the idea that some people are too young to know what they are agreeing to, so the decision should be made by someone else who takes responsibility for them (most things), or there should be no decision because there doesn't need to be one (voting).
We just need to refine our understanding to reflect the reality that as old as you may get, you will never understand some things.
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.
Talking about it outside of the specific conflict, is disingenuous. Everyone understands how important Autonomy is. That's part of the issue, not a supporting argument to value it over the health of a patient. If there's no patient, there's no Autonomy either.
The point of autonomy isn't to treat the patient as the most knowledgeable person in the room, but to present the options, all considerations and drawbacks that you're aware of, answer any questions, and then ask them to make a decision. If you think that patients aren't smart enough to understand the implications of drug side effects and weigh the costs and benefits of treatment versus the original disease, then I really hope you're not a doctor. And I really really hope you're not my doctor.
The idea itself isn't that controversial - age of majority laws for contracts, voting, and even medical treatment clearly acknowledge the idea that some people are too young to know what they are agreeing to, so the decision should be made by someone else who takes responsibility for them (most things), or there should be no decision because there doesn't need to be one (voting).
We just need to refine our understanding to reflect the reality that as old as you may get, you will never understand some things.