The future I see is that it gets rearchitected such that each app will correspond to an android app that way it follows the Android model properly. The current model of shoving everything into the same app is going to continually run into problems and is not the right way to do it long term. So essentially there will be a tool to easily convert a freedesktop Linux application to an android one.

In regards to this new package name registration whoever is running the repo of such packages would register a new package name for each app.