I was never very convinced that a 787 which managed to get airborne (suffering a tail-strike or a runway overrun would certainly be a possibility), would not be able to climb away on two good engines, regardless of the flap setting. There is a good demonstration of the takeoff configuration alarm from a simulator, it would be very difficult to ignore, and unlike some older airframes, the exact reason is displayed on the MFD.
Incidentally in that video the aircraft rotates and climbs out without flaps set, I don't place a lot of emphasis on that though because, firstly the simulator is not real life, and secondly I don't know if the conditions the simulator were trying to recreate were at all representative of the accident flight.