The name value pairs in the environmentvariables.config file are used to replace the placeholders in other configuration files, such as web.configs, CustomerSettings.config, etc.
The SCRM\web.config file, for instance, has a node:
<add key="WorkflowUserPopupURL" value="@@VAR:Prodika.SCRM.URL@@/PopUps/..." />
We replace the @@VAR:Variable@@ with the matching variable value from environmentvariables.config.
So if you have customized the web.config to add a custom placeholder, then you can add your own name value pair in environmentvariables.config and it would be replaced