First thing you need to know is that this behavior is fixed in Civil 3D 2015.
For those of you using 2014 and older, it turns out that the source of the switch isn't the layer in the source drawing, it's the default layers you see in the Network Properties command, and they can't be changed if it's a data reference.
So the workaround is to set the layers in Drawing Settings, create the reference, and then change them back. You are forcing the network to capture the layers you want at the time of the reference. It works...try it!