That all sounds very sensible, Bose.
However, while your ATO approval may have worked along those lines, the template manual differs:
At the beginning of the template manual it offers completion guidance, stating that text shown in blue is for guidance, text shown in red is where an ATO will need to provide their own specific information, and that where it is "required for the ATO to show its compliance" the text is written in black.
The CAA policy statement on 67 hours minimum TK classroom study is written in black.
MEL - Agreed, I hadn't spotted the non-mandatory elements. However, it should be noted that if the aircraft is also used for commercial air transport then the enforced MEL and limitations, in entirety, also apply to flight training.
Exam invigilators - The text (in black, i.e. mandatory according to the intro blurb) states: "The examination will be completed under the supervision of a Ground Examiner approved by the competent authority for the purpose. Candidates are not to be left alone in the examination room whilst the examination is in progress."
While the individual(s) who processed your ATO approval appear to have exercised restraint and common sense, the individual(s) who wrote the template manual appear to have a different agenda.