Yes, I see how that might be an issue. If you apply a simple 2D Vornoi to each individual face of your box, you’ll run into a problem, where the Vornoi cells at the border of each face don’t align with/correspond to their adjacent faces from neighbouring box faces. I imagine that would be pretty hard to remedy, so you should probably stick with the 3D Vornoi.
In general, the Vornoi pattern mostly depends on the positions of the points that it’s generated from.
If you are dealing with a rather small object, I’d probably bake the desired number of random points to Rhino, rearrange them until you’re satisfied with the resulting, new Vornoi.
Another option would be to relax the points with Kangaroo. Imagine each Vornoi cell as a circle or sphere with a certain radius that gets rearranged until each sphere isn’t intersecting other spheres anymore, thus relaxing the whole pattern. This is often referred to as circle packing. However, the resulting Vornoi pattern will become less interesting or random.