At my airline either is fine. Most guys click off the autopilot and autothrottle at the same time. But you can fly manually with the autothrottle engaged (manual crew coordination procedures apply). For the wind correction factor you can apply Vref + 5 if you plan on disengaging the autothrottle at 50 ft. agl (As long as there is no performance decreasing windshear reported).
With the autothrottle OFF the Wind correction Factor is ½ headwind + full gust value (min. of 5 kts, max. of 20 kts). So in windy conditions and runway length being a factor, it represents an advantage in flying with the autopilot off (in case of non-precision approach) and the autothrottle on. In these conditions it is true that you have to be right on the ball to catch the excesses in the a/t system, as pitch moment can be quite impressive. In my experience it is quite manageable. When both engines are running and no snags on the autothrottle the a/t arm switch always stays ON. For speed protection and for the thrust setting on the go-around.
Also in the thread it was mentioned that autopilot can only be used in conjunction with autothrottle. We are CAT I autoland with two or one engine operating with a/t u/s (and with only one running we have the autothrottle arm switch in OFF). And just flew a flight with the TMC u/s, and TMSP auto mode u/s. So manual thrust from beginning to end (was only a ten hour flight). It is still just an airplane.
Nonetheless it is always interesting to see what all comes out of the basic document that Boeing supplies and what our own pilot engineers in the flight technical, and training departments come up with.
Regards, O.