Thanks for the detailed write-up 
Will this affect “absolute” paths to files in a plugin used in a theme component? For example theme components that work with the layouts plugin all require helpers in the layouts plugin itself like this
requirejs('discourse/plugins/discourse-layouts/discourse/lib/layouts')
See for example, the layouts category list widget.
It seems the path change here brings it in line with the namespacing of assets in the plugin asset pipeline (using theme ids instead of plugin names), and that plugin asset paths used in a theme component will remain the same. And that a require like the above will still work. Is that right?