The vanilla world border operates under the assumption of linear chunks and limited height. While this works fine in vanilla for obvious reasons, this reasoning falls apart with unlimited building height for other obvious reasons - they are incapable of limiting player positions on the vertical axes, which may be undesirable for certain custom servers running the mod. As such, it would be advised to make the world border exist and be configurable as a vertical boundary as well.

Perhaps worth noting is that forcing the world border to be a cube like it currently is forced to be a square may end up being overly restrictive in many circumstances - some gameplay videos have showcased modes with massively restricted horizontal movement but complete freedom on the vertical axis. Forcing a cube would make cases like these an impossibility with Cubic Chunks, so it may be advisable to modify the world border as to operate on two or three diameters rather than one, to allow for vertical bounds to be customized individually of horizontal boundaries as well as to possibly allow for the horizontal bounds to be newly customised independently of each other as well.