There is a big difference between flying around privately (which is covered by the law) and operating as a commercial operator. As, in this case, an airline you need to have a FOM in place which determines the way you are going to operate. The FOM is not a simple company regulation. It does get approved by the country's aviation authority and becomes the law. By not operating according to the FOM, one operates outside the legal regulations and ultimately outside the law.
This is due to the fact, that the FOM in general has to be at least as restrictive as the law, BUT in many operations certain concessions have been made in certain areas of operation, which are actually less restrictive, than the law. For example, a country's air law says, crew rest time has to be at least 12 h or as long as the preceding FDP and it can be reduced to a minimum of 10 h.
An operator needs crew to fly an evening flight to an outstation and leave the next morning. Under normal circumstances this operation would allow for 11 hours crew rest, but in case of a delay, this would mean, the morning flight would be delayed due to the crew's rest period and screw up the whole rotation for that aircraft during that day, leading to next evening flight being delayed and so on.
This operator approaches their DCA with an application for dispensation. This dispensation says, the crew's rest period can be reduced to 9 hours AT ACCOMMODATION under the provision, that the following day this crew will only fly back to it's home base (1 sector, about 3.5 -4 h FDP) and have a local night and may not be dispatched before 06:00 local time the next day.
In other words, the operator can get a dispensation from the air law's FDP regulation on the one hand side, but restricts himself in turn to be a lot more restrictive on FDP the next day.
If the operator would now make use of the first part of the dispensation and allow it's crew only 9 hours of rest, without allowing the FDP restrictions the next day, that crew would theoretically still operate within the air law's FDP regulations.
They will in the end however violate the air law and DCA will go after the crew members for that.
If one now looks at this departure aerodrome in question, one could say it is not safe to operate a B737 out of there, since due to lack of facilities no T/O alternate would be available in case of an eingine failure just after V1. The a/c might not be able to gain enough height to safely clear the mountains. In order to make provisions for this case, the operator has put the twilight minus 30 minutes rule into their FOM, which has been approved by the NZ CAA and has become part of the air law, which has been violated by that specific Captain.
The very same person might have been legal to fly the same a/c type out of the same airfield at 18 minutes before twilight, if he would have flown for a different operator, which might have put different restrictions into it's FOM, e.g. payload restrictions in order to achieve the minimum climb gradient required to clear the mountains in IMC / or at night.