Originally Posted by
CPH-Flyer
I'd be more curious to where it is in the transcript of communication between tower and pilot....

Well I think I have seen many versions or interpretations of what was released, and this was on Bloomberg and other places. I have not investigated as to whether it is a true and accurate translation but here it is:
At 17:45:11 JA772A starts to communicate with the tower. Which is 10 seconds after JAL516 has been given clearance to land. Perhaps another hole in the Swiss cheese lining up even given that the "taxi to holding point C5" is unambiguous.