Why then does the checklist not necessarily follow the same order as the flow, to me this keeps things simple ?
Great question.
No real simple answer. But consider this....
Pre landing checklist. What do you want to ensure? The cabin is secure, the aircraft is in landing configuration.
You could call the checklist in order of 'flows'. That is, call it as you suggest, in the order in which tasks were done.
You could call the checklist in order of 'killer items'. That is, call the item of highest importance - if it is
not set, will pose the greatest risk to the safety of the flight in the upcoming manoeuvre.
That way, if the checklist is interrupted by ATC call or other threat and not resumed.....
If you are interested, plenty of stuff out there on checklist design. Try Degani and Weiner from NASA. Google them.
"Cockpit Checklists - Concepts, design, and use" would be a good starter.