I think people are not reading 40.13 clearly, read it carefully: "40.13 If the race ends whilst the safety car is deployed it will enter the pit lane at the end of the last lap and the cars will take the chequered flag as normal without overtaking."
So, deap breath, when does the race ends? On the end of the final lap right... so, safety car WAS deployed on the final lap, they have to take the chequered flag as normal without overtaking, SC got in cause of the 40.13, green flags were waved because of the new SC line, but they still have to follow the 40.13 rule, green flags does not mean the same thing in that final lap, they just mean the safety car got in the pits.
In Australia they did not waved the green flags, because there was no SC line in the pits, they would wave them after the finish line..