Non adjusted FMC speeds are based on a "balanced field" for the weight and not the specific runway.
If its your policy to use optimized Vspeeds or account for the clearway/stopway you will have to adjust the FMC speeds accordingly. However, I would say that it negates the usefullness of the FMC if you need to overwrite it every time, might be a good time to assess your company policy.
In our case, we dont account for optimized Vspeeds, clearway/stopway. FMC speeds are only adjusted for MEL's and contaminated runways.
Mutt.