3D layers that share the same position are always a little dodgy. Apparently, in your specific setup, the layer showing up on top changes with the rendering engine. That is not surprising. I just checked it on my system and I could get random results with 2 shape layers filled with the same color but one has a stroke. Depending on which layer was selected at the time one may pop in front of the other when changing to the C4D rendering option.
It would not be good practice to put 2 overlapping layers in the same plane with either rendering option but I don't think it is a bug, I think the top layer depends on when the rendering engine gets the layer info. I can make the bottom layer end up on top most of the time, but sometimes, it stays on the bottom.