In the Takeoff Shift field (TO SHIFT) you can enter an offset in meters if you plan to start your takeoff roll at an intersection and not at the runway threshold.
Internally, in the real aircraft, the aircraft position is updated to the runway threshold when you apply takeoff thrust. If you are actually further down the runway and not close to the threshold then the internal position has an error which translates to a position error once airborne. For more precise navigation, in case the GPS is lost for example this can make a big difference.
This is not simulated though, so you don't need to worry about that.