@Joe Thank you for reaching out to Microsoft Q&A, apologize for the inconvenience caused any on this.
For Python on App Service Linux you should not use methods like FTP or ZipDeploy (without the use of Oryx) to avoid improper deployment since the Python environment will not be built, thus causing errors like ModuleNotFound or others - since pip install is not ran in these scenarios as mentioned in this documentation here.
If you want to add the missing Package through the custom start script you need to create script file (.sh) under /home directory and add the path of script file (/home/file.sh) to start up command(In general settings under configuration in the portal) to keep your package persistent even after the restart as well. Here is the reference document on configuring customer start script in python apps.
I would suggest you follow this documentation steps to deploy Django Deployment on App service.
Feel Free to reach back to me if you have any questions on this.