I don't see any difference between using any of the the runways.The longer one or the shorter one.
The Fact that I am using Flex/ATM on the longer runway means that I am going to consider the entire length to be usable in case of a reject. Hence giving it a time line... Longer runway.. Lesser thrust... More Time to V1.. More Time to Vr... More Time to Get airborne... The amount of runways required to stop in-case of a reject on a longer runways will not necessarily be more.
Shorter Runway .... More thrust.... Less time to V1... less time to Vr... now incase I reject... I have lesser speed to bleed but lesser runway as well.
My performance Characteristics on both the runway short or long are going to be the exact same for the simple reason that I have used ATM/Flex on the longer runway. Some where on the first page some one wrote about the actual density and temp that being the only +ve side of ATM/Flex in terms of performance and Abslutely nothing else (Disregarding cost)
Also company specific performance usually has optimized V1.. to use the full runway ..Puting it simply just because you have a longer runway does not mean you can liftoff heavier.The longer the runway the more are the chances of an obstacle infringement. OTHH (Doha Qatar) rwy 34R/L have obstacles, in the case one would use improved V1 speeds for takeoff the weight penalty is more than unimproved v1.