I'd typically deal with this by exporting the functions to be ran as entry points in the the setup.py file, and then use whatever configuration management tool

I'd typically deal with this by exporting the functions to be ran as entry points in the the setup.py file, and then use whatever configuration management tool I'm using (Ansible, Puppet, whatever) to manage the crontab file in /etc/cron.d. Ansible's cron module makes this especially easy.