OP here. Yes, some of the stuff we deployed was packaged as .deb files - after vendoring all the dependencies.
Now when we build our Debian package (debian/rules):
override_dh_virtualenv:
dh_virtualenv -p myproj --use-system-packages
[1] https://github.com/spotify/dh-virtualenv
[2] https://packages.debian.org/jessie/python/python-virtualenv