Popay, respectfully I think you are tying yourself in knots on this one.
The flight was at the planning stage scheduled to be 11:45 with a one hour preflight period giving a total FDP of 12:45.
The flight on the day was actually 12:12 plus one hour prefight. In other words What actually happened was an FDP of 13:12.
When the roster was produced it was presumably based on an average block time of 11:45 and there was no real way of knowing that on the day the actual block time would be longer.
The schedule could not be based on an unrealistic block time as this would constantly result in discretion reports that would arouse the interest of the authority. Nevertheless discretion in this example is based on what actually happens, not on what was planned to happen. It is this distinction you need to accept. The actual block time on that day was not planned. The schedule of 11:45 was what was planned. The trip time of 12:12 was what actually happened on the day.
I note also that you now say this flight comprised only 1 sector. If it was a 2 crew operation that would normally in fact count as 4 sectors, so I am assuming there must have been an additional crewmember on board to remove this restriction. In such circumstances that crewmember who must be a current type rated pilot would be a resource to provide crew rest periods to the other 2 pilots in any event.
All of this is acceptable, normal and happens every day. If you think your companies schedules are unrealistic and you have the statistical evidence to substantiate this to support that contention, then a report to the relevant authority may be appropriate, beyond that all I can say is this is acceptable for the commanders consideration. Does it matter that on the day the flight will require commanders discretion before it has even left base ? No not one bit, as long as the commander is satisfied it can safely be made having taken into account...etc etc.
The last question concerning the CAA and the commanders decision is irrelevant since he has done nothing wrong.