Lion-g,
Just to clarify a point or two, you state "As for autoland, the system will still fly Vref + 5 till flare height of 40ft AGL which i suppose, over the threhold.
". If you're referring to B777 (I'm guessing), flare height is indeed 40 feet, but Threshold Height is still 50 feet, thus, the flare begins after the threshold.
Again, assuming that you refer to B777, you would be aware from experience that a flare commenced at 40 feet for a manual landing would result in landing "deep", 30 feet (and less for braver souls) produces the most consistent touch-down at the 300M marker, thus, the 40 foot flare will be deep, requiring a longer landing distance.
Not a very scientific answer, but it may supply your answer sought.
Regards,
Old Smokey