S.F.L.Y
It is very interesting to me to see that actions were taken on the flaps (drag reduction strategy) prior to taking manual pitch control. It's probably a much easier mental process to give up on the initial flap setting than on the AP ILS approach. Taking over manual control of a critically low speed and powerless aircraft is a natural decision for any pilot. Why did it happen so late? My point is not to criticize the pilots, but to understand why they didn't take the actions we could expect in such situations.
if you would finally accept that flaps 30 are just like huge airbrakes then getting away with such brakes is clearly the most important item when trying to stay in the air, especially that at some 400ft is a shade too early for a flare.
Until the AP disconnection at a very low speed, they probably were probably keeping hope of making a normal ILS. When they finally got the proper situational awareness the speed was already way to low and nose had to be pushed down. Fortunately the plane had just enough height to recover the few knots to neutralize some of the Vz.
You may be right that for some time the crew had waited to see the results from retracting the flaps. But i would not bet too much on the crew expecting to stay on the ILS path and make it to the runway securely as usual.
(1) AP has not turned itself - it was turned out by the control movement from the flight crew. (2) Nose was pushed down and at the same time they have used ailerons+possibly rudder to turn right (in order to miss the concrete runway surface to avoid fire)
They had made a perfect flare - you can see it from the main wheels crushed into the wings - but what is more important is that they had managed to keep the plane flying (arrested speed decay and made typical stall avoidance maneuver to gain the speed). With the vertical speed constantly increasing the higher the plane speed the better was the chance to glide to the ground instead of falling on it. And with higher speed the control movements had better chance of success.