>>IIUC the support for setup.py is transitional, i.e. "legacy support", for existing packages transitioning from distutils/setuptools/Distribute to packaging. New features should not rely on the existence of setup.py.

I know, the implementation way of scripts has nothing to do with the setup.cfg or setup.py, these two files are just different ways to offer configuration values. So just don't worry about that.

What the I try to express here is :
There are two kinds of configuration files supported in Packaging, and you can say it maybe a transition consideration from  distutils/setuptools to Packaging, but if you look into the documents of Packaging(you can generate it from the /Doc directory), you will get to know that Packaging has a more further and important consideration - setup.cfg and setup.py place different roles in a project, setup.py offers developers to set while setup.cfg offers users to edit in a cheap and easy way... Certainly you can set anyone of these two files to reach the same goal. Just visit /Doc/build/html/packaging/configfile.html to know more about the different roles of these two configuration files.