Pycharm: set environment variable for run manage.py Task
Another option that's worked for me:

Open a terminal
Activate the virtualenv of the project which will cause the hooks to run and set the environment variables
Launch PyCharm from this command line. 

Pycharm will then have access to the environment variables. Likely because of something having to do with the PyCharm process being a child of the shell.
I have moved my SECRET_KEY value out of my settings file, and it gets set when I load my virtualenv. I can confirm the value is present from python manage.py shell.
When I run the Django Console, SECRET_KEY is missing, as it should. So in preferences, I go to Console>Django Console and load SECRET_KEY and the appropriate value. I go back into the Django Console, and SECRET_KEY is there.
As expected, I cannot yet run a manage.py Task because it has yet to find the SECRET_KEY. So I go into Run>Edit Configurations to add SECRET_KEY into Django server and Django Tests, and into the project server. Restart Pycharm, confirm keys.
When I run a manage.py Task, such as runserver, I still get KeyError: 'SECRET_KEY'.
Where do I put this key?