Well, I guess that situation is typical, flight crew can't often see flames on the inside of the wing, between engines and fuselage, so they rely on cabin crew to alert them to what's happening, "down the back".
Airbus has complimented JAL crew on a "textbook evacuation", and I think the fact that all 379 people got off with no injuries is an outstanding effort, regardless of any errors on the flight crews behalf.
It appears the Captain of the Dash 8 may have been fatigued, he put in a sizeable amount of hours in preceding days, checking out earthquake damage and flying in supplies. He had also previously been getting takeoff priority, as a result of him carrying out disaster work.
Bottom line is - he was told ""JA722A Tokyo tower, good evening. No.1 taxi to holding point Charlie 5". This is certainly not clearance for takeoff - but with inoperative red lights at holding point C5, the Dash 8 Captain obviously thought he was "No 1" in lining up to take off. The problems stem from ATC not using better U.S. style ATC terms, such as, "Hold Short at runway", which is clear and unambiguous. Add in the fact that runway incursion warnings were also not operating on 34R, and there's all the holes lined up.
Also, sitting on a well-used runway for 40 seconds is not good. I've regularly heard "takeoff without delay" from ATC, as soon as we lined up on the main runway.