Originally Posted by Pickles

My experience also. Bass-ackwards, if you ask me, but it looks like to be driven by NRT, not by JAL or the airlines. I was standing by the door and had a chance to view the process. Basically, they let all terminating passengers off first, and then they close the door to the arrivals terminal and open a side door directly into the departures area for that gate. The connecting passengers all file through there, skipping the usual security check once in arrivals area to be let back into the departures area. I watched the JL elves on board and on the ground make sure every terminating passenger is off the plane and in the arrivals area before letting any of the connecting passengers off. Onward boarding passes were checked before allowing passengers through into the departures area.

I don't see why they couldn't run the process in the opposite order, lowering blood pressure levels overall. I cannot confirm, but I am pretty certain that onward connections are held for the inbound passengers. My own flight was delayed somewhat, and my onward connection was consequently pushed back also. The Japanese announcement apologizing for the delay explicitly mentioned "late arrival of the incoming aircraft", which wasn't the case as the incoming aircraft (per Flightaware) had been sitting at the gate for hours.