Why are django projects python packages?
The core of a project is a settings.py and a root urls.py. Both of those are Python modules, thus they need to be importable somehow. You can put the project directory directly on the Python path and thus make them importable as top-level modules, but that's arguably even worse practice. Better to have the project be a package and the settings and urls be modules within it.
Why aren't they simply directories? Any good advice says to keep as much as possible in the apps and not to couple them to the project. The very ability to import an app as project.application discourages this. Why does django-admin.py create the __init__.py at all? The project is perfectly useful without it. What is the justification?