To add to an interesting discussion!
My belife in reading CAP371 is the decision to use discretion can only be made:
1. By the commander, after 'consulting' the other crew members.
2. Needs to be made at the point it is required.
Taking the original case, the 'company' could insist that the flight is commenced and ,if at the point during the flight that discretion is required, is not considered appropiate by the Captain, then a diversion made.
The CAA are happy for you to depart and it could be the fact that due to 'unforssen circumstances' the flight is actually completed within the normal FDP. I have seen this serveral times over the last years that a bit better wind and a few short-cuts keep in within the limits.
The CAA will have a serious issue if you use discretion <20% of operations of a route and would then audit the whole planning process. So I doubt there are many cases were there is a different motive and if there was the CAA would probably find it.
This is normally the biggest issue on the agenda of any CAA FTL audit and therefore one of the most focus of crewing depts.
There is a bigger issue that the aircraft can complete longer sectors than the FDP and often the use of inflight rest is a joke as the aircraft is not equiped for adequet rest. CAP371 allows rest in a seat which again is a joke - but how can an operator justify $1m spend on something that may happen 1 or 2 times a year (especially on an unplanned basis)?