I have followed what I think is the documentation to create a setting. A simple class, and a boolean setting. It creates a .config file and I can fetch the boolean, update it, etc. And I can see it updating the .config. On local. When I go to DEV/TEST with the 3 files as a changeset and build I don't even see the config section in backend admin->settings->advanced.
public class SystemMaintenanceConfig : ConfigSection
[ConfigurationProperty("Maintenance", DefaultValue = false, IsRequired = true)]
public bool Maintenance
this["Maintenance"] = value;