Hi,

The 3D version distributes nodes no worse than the 2D one, but uniform distribution in 3D space does not guarantee that the subgraphs will look separated in a 2D projection, even if nodes from a subgraph were not getting into the bounding sphere of another subgraph.

I suppose you can avoid both overlapping of subgraph bounds and ensure they are separated in the 2D projection by arranging the full graph in two passes. In the first pass arrange each component on its own in 3D, measure the size of its bounding sphere, and create a virtual node of the same size in a temporary diagram. Then arrange the temporary diagram in 2D, and offset the original subgraphs to the positions of the virtual nodes that represent them.

You could use 3D layouts in both passes if you don't care about separating the subgraphs in a 2D projection, but only need to avoid overlap of their bounding spheres in 3D.

I hope that helps,
Stoyan