I think there is a rather simpler explanation, which is due to how blender handles layers and output in the first place:
as you mention there is only one render path in blender, and despite all the enabled layers being rendered, only what you see in the image viewer is saved. You can see what happens if you click Render Animation in the render panel: you will be able to switch layers in the picture viewer toolbar, yet only the active render layer has been saved to disk.
To my knowledge the standard way to deal with multiple output in blender is via the compositor File Output node:

- In the node editor, please activate compositing (middle icon) and enable the Use Nodes checkbox
- Add another render layer, you can duplicate the default node and change the layer in the drop down at the bottom
- Create a File Output node. In the sidebar add an input for each of the layers you want to save to disk
- Connect the Image output of each render layer to one of the image handles of the output node. You can rename the handles accordingly so that the saved filename makes sens
Optionally, you can use separate image nodes with different base paths, or save channels of a render layer to file using the same logic. Royal Render will still display the main output, but you will be able to save all your layers to disk. Unfortunately the way blender rendering is designed makes it difficult for us to implement a consistent render layers logic. We are waiting for blender 2.8 to add some RL management to our blender configuration, but you are very welcome to give us some input on how a good blender workflow could be implemented
Hope this helps, kind regards
Paolo