I think technically Japan does not issue visa on arrival. All Japanese visa are issued prior to arrival outside of Japan. Immigration officers at arrival airport in Japan can issue “Transit Pass” on case by case basis. From what I read, conditions of this Transit Pass can vary and seems to be highly dependent on a passport issuing country of a passenger.

One example I read that a passenger had the Transit Pass issued and stayed at a hotel near the airport. This passenger was free to leave the hotel room and wonder around the town. Another example I read indicated that a passenger was escorted to a hotel room by an officer from an airport and there were constantly a guard outside of the hotel room and a passenger was not allowed to wonder outside of the hotel.

Also, if it became obvious that you will miss the connection in Japan and have to overnight in Japan but you do not have appropriate visa, then JAL may not allow you to board the flight to Japan at the departing airport.