....on the way down from BNE on Monday we took off using a shortened runway ie the pilot didn't taxi all the way to the end of the runway before lining up, he entered off of one of the taxiways part way down. As we were doing it I remembered an expression that I've heard along the lines of "useless things in aviation include altitude above the plane, runway behind you, and fuel left in the bowser". Presumably the pilot is responsible for electing a shortened takeoff, why wouldn't the pilot always use the maximum amount of runway just in case a stop was required at the very last moment?
You need to change the way you are looking at it. We calculate a V1 figure for every take off, but we are not looking for the highest refusal speed possible, but rather, the lowest go speed. In almost all cases getting airborne with an issue is a better outcome than trying to stop from high speed. On an infinitely long runway, V1 would be calculated so that if we stopped from that speed, it would take the same distance as continuing, with one engine out, and reaching 35 feet. The upshot is that on that infinite runway, this calculation would discount any runway that it did not need to balance the two distances.
Beyond that though, use of a shorter runway, may require more power, or a different configuration. Configuration is neither here nor there, but using the least power possible is good for the engine. Countering, that, if everyone used the full length, then it would be quite a nightmare for ATC, and everything would slow down.
If it's extremely windy, they will most likely use TOGA anyway (because of the risk of wind shear), so derate becomes moot.
Looking at the A380, we almost always use 24L departing LA, even though it is relatively short for the operation, and requires TOGA power. Why? Because the time taken to use the alternative 25L is too much of a cost in time and fuel. Departing say, London, I'm quite happy to use a shorter choice, as long as the power required gives at least some derate (and going to Dubai, any start point that we might use would give the maximum derate).