Remove the onboarding - system fields link

System fields are a great way to restrict student information from certain user types. In an enterprise RTO we have a lot of personal information of our employees in our database therefore we use the system fields to restrict personal information to only certain user roles. We have discovered recently that restricting the system fields visability also means that our users cannot update their own information through the onboarding feature and they get a continous 'unable to save' error when they are enrolling in training for themselves. 
The only way around this is to not utilise the system fields functionality and allow all users to view personal (private) information. This is not a good solution and negates the purpose of the system fields.
Am I missing something? 
Could the system be updated to remove the system field restriction to their own profile so users can both be restricted from seeing others personal information but can still update their own.