Email replies regardless of whether they are from collaborator agent or not should be treated as a normal reply, they should not be converted to a private note which is then not in the reply to the customer, this is then unprofessional.
The only time emails should be seperated from the main email thread is when a forwarded email chain has been created. Again forwarded email chains should not be treated as private notes and whould be better handled do they are easy to view and filter out from other information.
Having too many private notes is confusing and adds complexities to automation rukes