Hence, I thought that using the :unix layer, would have the effect of "recognizing" the proper endings

The key word was "adding". You were causing your handle to have layers :unix:crlf:unix.

Furthermore, :unix does not refer to file formats. See PerlIO for definitions of the layers.

If I understand right, using just binmode without argument is equivalent to specifying the :raw layer.

binmode without argument is not currently equivalent to specifying :raw, because :raw doesn't currently behave as documented. You want the documented behaviour, so you want binmode without arguments.