The reason for the recommendation to disconnect the a/t if flying manually is mainly the fact that ,especially at low weights, you may encounter some turbulance at low height (most critical during flare ) and the a/t , sensing AOA approaching alpha floor,will command full thrust very rapidly.
Some of our guys used to keep it in ARM ,untill a few got full power commanded by the a/t,during flare...not a pleasant thing,believe me.
If i/m not mistaken ,the Bus,which uses the a/t to touchdown in 'manual' flight disables the alpha floor protection at some height ( 100',I think)
Yflex: if you keep the a/t on to touchdown ,at 27' it will go to idle thrust,just like on autolands.It has a 'mind' of itself,independent of the autopilot.