So, I think that the best way to address this would be to allow it to be mostly open. The default is for all notes from the doctors and patients visible to everyone; but doctors can write "hidden" notes that only other doctors are able to see.
In a lot of ways, I see this like a public bug tracker. For bug trackers, it's generally best for everyone to see all changes, to be kept up on what's going on and be able to most usefully provide extra information. But for security sensitive issues, or internal discussion that involves things that the end user needn't know about, many have a way of posting "protected" comments that only certain privileged users can see.
In general, you have to put a certain amount of trust in your doctor.
They are helping you make pretty life altering decisions. Now, there is a bit of a cultural barrier where they aren't used to the idea of patients being as involved in their medical care, but on the whole, they are there to help you.
If you're really all that worried about your doctor writing lots of secret notes and not letting you see them, even once there's a system in place to allow you to easily collaborate with them, maybe it's time to get a new doctor?
And what if doctors just start writing everything in the secret notes? The situation sounds exactly like what has happened with the US government classification system.
How does hidden help? An honest response to a hypochondriac is pretty obvious to any other doctor. 100x "patient complains of y, tests show no evidence"
I know more about pediatrics than about other specialties, but there are several use cases for hidden commentary in pediatrics. One is commentary about how to handle the patient's parent, who may, for example, be well-meaning but verbally abusive to staff, and the practitioner needs to be know to be constantly reassuring to avoid confrontation. Another includes notes that are about the patient, but not legally allowed to be seen/read by the parent (who otherwise has rights to a child's medical record in the US until age 18), such as discussions around sexual activity or birth control.
In a lot of ways, I see this like a public bug tracker. For bug trackers, it's generally best for everyone to see all changes, to be kept up on what's going on and be able to most usefully provide extra information. But for security sensitive issues, or internal discussion that involves things that the end user needn't know about, many have a way of posting "protected" comments that only certain privileged users can see.