Ya using voxels was definitely a big drawback to my approach here but was more intended to just see what's possible.
I think a better approach would be something similar to the StructureNet paper I mention in the post and use graph based models to actually attempt to capture the topology. But they did it with super explicitly defined part trees as training data the hard part would be finding a way to do that in a unsupervised manner so you could actually make use of the massive amount of unlabelled 3D models available.