A coincidence?
From my point of view I am using the nodes as properly as I possibly can. The meshes are not meant to be instanced. There is one mesh per voxel-object. The mesh can extend over tens of thousands of individual voxels, containing several times this amount of faces. I have to dynamically decide wether to draw (add to buffer) or leave out faces that are hidden by neighbor-voxels etc.
I can't use 10000 individual nodes for that, unless I want to make a slide-show. Have you worked with particle-systems? They work very similarly, although they only have a single material. If you created one node per particle...
I need one buffer per material (several, if the number of vertices gets too high). Even if I used an individual mesh & node for each, where would I place them, if not at the voxel-object's origin? All the face/vertex data added has to be relative to something.
I am not going to believe that the fact that everything works flawlessly with standard materials, no matter how many, is pure coincidence.
