Publish Document from RQM and select Global Config

There is no option to present the GC picker (from where you can select the GC) during report generation through RQM. If you see "Edit Configuration Metadata..." window in RPE Studio, there is no option to set GC. You will only find Identifier, Display and Request URL fields. A GET request is done on Request URL and from the data returned, XPath corresponding to "Display" is what you see in the drop down and "Identifier" is used to configure the data source.
You can rather use an external variable in RPE template, where user can provide the configuration URL. This variable value can be appended as oslc_config.context parameter to Request URL; for this you need to use a Data Source Configuration element in the template.