Perhaps they had no time to exercise spatial awareness (visibility issues?)
I think I remember that they were in or near a storm at the time. I don't remember whether it was day or night.
I think you might be right, I think there was inclement weather in the area. But I seem to recall the flight was in daylight.
And as far as the yoke vs side-controls, a fighter pilot is comfortable with the latter, but in a big plane, I would think the yoke rig would be preferable.
