1549 was into a smooth river and there was a pilot in control and he had power. Realistically MH came down after running out of fuel, with no one controlling it. Auto pilot wouldn't have been able to detect the water level and who knows what it would have been trying to do with no power and a glide decent.
The only argument where MH comes down in the Indian ocean with a live pilot at the stick would be either a suicidal pilot or a pilot under duress.
More likely it hit the water nose down in an unpowered glide. It may or may not have hit flat, who knows. But it would have been coming into rough water which makes it much more likely it tumbled.