No it doesn't enforce that, it just doesn't like you have "base" layer in two locations.
see how whole structure and layers work Layered Distributions and Module Path Organization | JBoss Developer
You should probably create extra layer with all your subsystems in it.
Thanks for the response. I guess that most of my additions is really add-ons and should be placed as such.
I can not get it to work. Do you know of any existing example that works?