The margin is for example that the plane must not just be able to fly, but also reach a minimum climb gradient to clear obstacles with a bit of safety margin. There is also an allowance for the time it takes from calling abort to actually hitting the brakes. And for example headwind is part of the calculation (it makes the takeoff distance shorter) but only 50% of the headwind is used in the calculations.
But all of those margins are not for the crew to use, the crew must just execute the procedure exactly as trained which means at V1 you're committed to continue the takeoff. And before V1 in case of an engine failure you have to hit the brakes to make sure you can stop before the end of the runway.