I have another issue with transparency and 3D Objects, but only when I use the "Fog" effect.
It seems that transparent objects prevent the fog to be shown behind them. As workaround I've created another layer without fog; I change the brightness of objects on this layer when I move the camera, but you can see that the light is not exactly the same as the objects on the "foggy" layers.
You can find the issue in the "Foggy outbreak" template as well. Any way to fix it?