dh-virtualenv says that the data_files directive inside setup.py is not the correct place to specify files that will reside outside of the python source root (e.g. /etc/foo/config.ini, /etc/systemd/custm.service), and that you should "[use] Debian's install files to move them into the correct location".
Is it possible to configure the install directive when the debian directory is generated using make-deb?