Looks like you will have to SSH and run your scripts. Your deployed app version can be found here: /opt/python/current
One another option is to have a custom (and secret, may be) URL mapped to this in your flask app. When you hit the URL, then the execute the required commands.
If on the other hand, the scripts are required at app deployment / server restart, you can use the .ebextensions: http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/customize-containers-ec2.html#customize-containers-format-commands
Here you can setup various actions to be run before app code is run.