You can create Azure KeyVault secrets from ARM templates. Can you also create settings in Azure App Configuration from ARM templates in the same way? I can't find any documentation for it if this feature exists.
It doesn't exist yet but we're working on it! It should be coming soon and when it does we'll be sure to put how to do it in our docs.
Edit: Support has been added in the 2020-07-01-preview API version. Here is the documentation.