I have three layers in a map that have the same name for certain reasons. In the Apply Symbology From Layer tool, it clearly delineates the different layers in the map in the layer parameter pull-down menus by adding :n to the layer names. However, it will not work if the input layer and symbology layer have the same name, even with the :n distinction. It says they are basically the same.
I think this should work even the layer names are the same. The layers are different and the operation makes sense.