PC, attempting to answer some of the questions.
The ‘pad’ should be considered a safety margin which provides some ability to minimize the risk from variations in normal operation. It does not ensure risk free operation, e.g. you cannot expect the margin to cope with several extreme variations (fast, high, and long) all at once, nor significant variations in surface conditions or weather (crosswind), especially if wet.
The Captain has responsibility for the safety margin. In EU operations s/he has to ensure a safe operation (pre landing EU-OPS 1 ref …?).
A margin of 60% landing distance is required for dispatch. A Capt would have to justify how an operation would be safe if less than that margin were chosen. It might be justified in abnormal circumstances, but in normal operations, less so.
The landing performance is based on crossing the threshold at Vref; pilots should aim for that speed, but as above there will be ‘small’ variations. If other operational decisions require a higher approach speed such that Vref will not be achieved, then the landing distance required should be adjusted to maintain the safety margin.
Wind and gust additions are usually according to manufacturers’ recommendations, use those, and consider adjusting the landing distance.
There should be no need to duck under the glideslope (nor any thought of doing so), as this reduces other safety margins. The aim is for a stabilized approach, but some manufacturers and operators allow a small speed reduction when approaching the threshold to achieve the target threshold speed, i.e. when a safe approach is assured.
Certification landings do not involve exceptional high rates of descent or difficult maneuvers. Manufacturers are required to recommend a normal landing technique which does “not require exceptional piloting skill or alertness, nor involves excessive vertical acceleration, tendency to bounce”, etc, (CS.25.125). Thus manufacturers may be limited in their methods of obtaining performance data, but it is most unlikely that normal operations will be able to reproduce an equivalent distance, either in flaring and touchdown, and perhaps also in braking.
The 60% safety margin should be considered a normal minimum, particularly on wet runways where there can be many more unknowns and greater variability in the conditions. Accident statistics and some technical reports suggest that a larger factor than currently used is required in adverse conditions in order to maintain the same level of safety. Note that in some operations on contaminated runways there may be little or no margin.
Do not equate landing distance safety margins with any other operational safety factors, particularly for takeoff where there may be no margin; – JT will give you full Chapter and Verse on those issues – search for relevant threads.