How can I read the Environment Properties from my AWS Elastic Beanstalk Application found here:
Configuration > Software Configuration > Environment Pr
It looks like this behavior has changed in Elastic Beanstalk. The docs now say
Settings applied in the AWS Management Console override the same settings in configuration files, if they exist. This lets you have default settings in configuration files, and override them with environment specific settings in the console.
So you can now use the same config names in your web.config and in the Elastic Beanstalk config, and the Elastic Beanstalk values will override any in your web.config. It looks like EB simply adds new entries to the web.config file, so there will be two entries for any values defined in both places. Since the EB-added entries are later in the file they take precedence.