A project is a collection of one or more apps. When you create a project by default, a default app of the same name is made within a folder of the same name. Thus you end up with a nested folder structure like /myproject/myproject
.
I suppose why it doesn't dump all the default/root app files in the root of the project folder is because that would make it a bit more complex to manage multiple apps. The default app is structurally the same as other apps. Django relies on certain conventions, including special filenames and certain folder structure, to tell what's what.
In a structure like this:
myproject
/myproject
/myapp
/anotherapp
You can refer to myapp from within myproject, and Django can locate myproject very cheaply due to these folder conventions (and likewise the other way around).
You can tell which app is the default app by examining manage.py, which will have a line like this within def main()
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'myproject.settings')