Yes you can export the whole scene as a spritesheet.
128 limit is due to performance. I could probably work around this to support even bigger sizes but it's not the focus of this software - it stops to look like "pixelart" at that level of details and you should consider more effective technique if you need voxel objects of that size - probably low poly 3D would be a better fit. SpriteStack is for making game objects like units, chracters, buildings that look like games from 90's