We had a question about that issue some time ago when a colleague trying to do a 90° lineup on a non-standard cleared 4000m runway slipped into the grass on the opposide side (the airport only cleared 10m around the yellow line). The interesting answer from boeing was that a minimum distance lineup is considered in the performance software with a usual distance between end of runway and maingear between 2 and 6m. The difference between actual and assumed temperature is taken into account and with derate plus assumed temperature plus improved climb speed schedule a 4000m runway can become very short indeed even for a lightweight 737-700.
Lately they introduced an option for increased lineup allowance which allows distances up to around 100m from the end of the runway, how much is shown for each runway. However, it is the operators choice if he makes that option available or standard for the performance calculation.