A Workspace or a Project can hold Schemes.
I've never used Xcode Server, so I don't really know. In Xcode it comes down to what you opened, the project file or the workspace, I'm guessing something like that still applies is setting up Server.
As to why GTM only shows this, it are the other pods ObjC? Do you use them all in the same way? Bridging headers, etc. Since you are using CocoaPods, it is creating the project in use for GTM. Maybe try asking some other places where folks might know specifics about using CocoaPods with Xcode Server?