The productivity and efficiency of port operations strongly depend on how fast a ship can be unloaded and loaded again. With this in mind, ship-to-shore cranes perform the critical task of transporting containers into and onto a ship and must do so as fast as possible. Though the problem of minimizing the time spent in moving the payload has been addressed in previous studies, the different heights of the container stacks have not been the focus. In this paper, we perform a change of variable and reformulate the optimization problem to deal with the constraints on the stack heights. As consequence, these constraints become trivial and easy to represent since they turn into bound constraints when the problem is discretized for the numerical solver. To validate the idea, we simulate a small-scale scenario where different stack heights are used. The results confirm our idea and the representation of the stack constraints become indeed trivial. This approach is promising to be applied in real crane operations and has the potential to enhance their automation.