Because command-line arguments have a default and are set after the environment variables are read, environment variables cannot be used with command-line arguments. They will always be overridden by the default or passed command-line arguments.

I have confirmed this behavior in production as well. Environment variables do nothing when a config file isn't used. I created a test branch where I removed the command-line setters like lines 189-190 above, and this allowed environment variables to be used again (but this disables command-line arguments entirely).

One possible way to fix this is using the flag library's visit method to get a list of only the command-line arguments that have been set and only updating those.