Personally I use layers in my templates so I never have to worry about what config.pro file has been read. But the "def_layer" config.pro optiongenerates layersdifferently than layers intemplates. It actually reduces layer clutter.
The config.pro option only creates layers when the associated entity type is created in the model. So there aren't any unused layers. In other words, if you don't create an axis in the model, the default axis layer does not exist. Also, if you open a model already containing axes, it will not create the layer until the next axis is created. It won't put previous axes on the layer either.
Since the def_layer option can/should be used more than once, don't put it in the config.sup file unless you want to prevent people from using it. The syntax for creatinga default axislayer is: "def_layer layer_axis 03_all_axes".
Good Luck