As with most this in aviation it will likely come down to cost. As mentioned airwy charges and the like.
Depending the loads to have you may be capped for a portion of the flight at a certain flight level. If this flight level is in a strong head wind then it may be more efficient to fly longer distances to avoid.
Depending on the flight planning suite the airlines use the crew will be presented with the route the airline wants them to flying based on whatever is most important to that airline be it cost or speed.