I would have thought if the student used his own version of checklist and it included ALL the parts of the CFIs requirements then the flight is still safe and they should not fail a test.
Just one point, why is hatches checked? The CAA have for years reported that an open door has been the cause of distraction and hence many crashes whilst trying to close it in flight. I was taught if the door opens during flight ignore it (and the noise) and do not attempt to close it (almost impossible on PA28s top latches) and land as normal.