Elixir is a compiled language. The only difference between .ex and .exs is the .ex file is compiled and written out as a binary file on the disk, but the .exs is compiled on the fly into memory and not serialized out.

The typical usage of runtime.exs is to read values from environment variables then config the application at runtime. So you don’t change runtime.exs, only the startup script that set those environment variables.

In most web applications, the majority of the configurations are admin changeable from the UI, and those are typically backed by the database. The amount of flat file configuration is kept low. We don;t want to restart the application too often, right?

config/config.exs is read during build time and config/runtime.exs is read during application startup. Both of them are evaluated only once. To change the config of your app while it’s running, you need to do a bit of work yourself. I don’t think Elixir provides any tools for that out of the box.

Be aware however, that there are quite a number of tools which only look at the configuration when they themselves first start up (which is usually at elixir-application-startup time), after which changing the configuration settings using e.g. Application.put_env might have little effect.
Check the particular tool(s) you are using to be sure if/when it reads the configuration.

(And generally speaking it is nice if tools are able to pick up new configuration at runtime, because it is not rare to want to alter how something behaves at runtime at all.)