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.
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>I think I understand that much. The point of setup.cfg is to do away with the completely ad-hoc nature of code that developers can put into setup.py, which prevents playing nicely with distro package managers. I'm fairly sure I've seen Tarek say that "for developers, no more setup.py" - in fact, I've just found where he said it:

http://tarekziade.wordpress.com/2011/05/22/packaging-has-landed-in-the-stdlib/

and also

http://pycon.tv/#/video/57 (at around 6:55 into the video, and at 8:30 - "there is no more setup.py" - meaning in the new way of doing things)

So the role of setup.py is historical, and the way developers customise installations is through using hooks. These work well enough, and I am currently using them in the nemo project which is a companion to the pythonv branch - see http://www.red-dove.com/screencasts/pythonv/pythonv.html