But suppose the captain said something like: "Look here, your landing was good, but it would have been even better if you had managed to cross the threshold below 50 ft" - would you disagree with him?
If you are asking me, then yes I would disagree. First, you are eating away on one margin (obstacle clearance), to increase another that needs no increasing (landing distance). Second, you change your profile in the last seconds of the approach, which may lead up to a long flare = nothing gained.
Boeing directly advices against doing so, as quoted earlier:
FCTM:
When visual contact with the runway is established, maintain the glide path to the flare. Do not descend below the glide path.
For downhill sloping runways the AFM landing distance is unconservative. Would it be wrong to use a glide path angle of -4 degrees when approaching a runway with 1.7% downslope?
Any slope affecting the ground roll would need to have appropriate corrections applied to the total LDR. A slope in prior to the touchdown point (normally upslope) doesn't affect the LDR, as the aircraft still doesn't have contact with the runway - pretty logical I'd say.