Be aware, the exported gltf models are heavily unoptimized at this point. The option for 3D model export is currently only meant for transfer into other apps for optimization or stuff like 3D printing where vertex count doesnt matter. You might want to check out MagicaVoxel or other alternatives if you want to make engine ready 3D models.
As i cant compete with such editors, i will try to make something in between of a 2D drawing app and 3D Voxel editor which can help in transforming stuff and also just trying to experiment with sprite stacking.