Actually, the final item on the shutdown checklist it is Battery Master only, and set 'as required'. On a turnaround, this would normally remain on, so as to avoid plunging everything into darkness and requiring a complete reset of the flight deck instruments/FMS. I can see flying with you would be a lot of extra work.
I would agree however, that best practice on an extended turnaround where the crew have vacated the flight deck, is to turn the 3 batteries off which would help to avoid just this kind of situation.