I do not see any problem in overriding the AT's in this case and I would agree that most pilots tend to use the AT's through the touchdown and this is very comon in some Boeing aircraft.
As I recall you moving on up
to the 777 soon. The AT system in the this airplane is very similar to the MD11 although it may react just a little quicker. Point here is that just becasue you have the automation working does not mean that you are not part of the solution in getting the airplane on the ground.
Where I flew the MD11 we encouraged the pilots that if they were inclined to turn off the AT's prior to touchdown, go ahaed and do it around 1000' AGL and get into the stck and rudder mode early in the game, thus not clicking them off at 100' and finding yourself not part of the game.