Yikes, thanks for dragging this up SR71, I had forgotten about it!
The easiest way is to deal with each item individually, I will add that we operate an extremely diverse fleet so my answers will refer to our aircraft in general and not particularly every aircraft type.
Stopway Not accounted for. Goes back to B707 days so I don’t know the rational behind it.
Clearway (a) Generally speaking, a large percentage of our operations use a generic takeoff chart for all runways in a particular airport, takeoff weight given for 4 temperatures based on the worst runway at that airport. Using this, there is no point in using clearways. (b) Some takeoff chart programs don’t allow clearway’s. (c) Airports in home country are long.
Increased V-speeds. Big NO NO, crews have no desire to use higher than required V-speeds. Initial aircraft/home base takeoffs were field length limited, therefore improved climb wouldn’t work!
The goal is to keep takeoff calculations as simple as possible, basic takeoff charts are used with the QRH/FMC V-speeds with minimum corrections. The desire to achieve this is usually greater than the desire to get the highest amount of “thrust reduction”, or additional payload!
Mutt.