File's Owner is not a real object in the xib file. It is a proxy object. It represents the object that will become the xib's owner when it is loaded. First Responder and App Delegate are proxies also. The first responder is the object currently on top of the responder chain. When the state of the application changes, another object might be the first responder. You use this proxy object to connect things like the File->Save menu to whatever object is responsible handling it at any given time.
The App Delegate is an actual object. It springs to live when the xib is loaded. As you can see in Interface Builder, it is connected to the delegate outlet of file's owner. The Application loads the MainWindow.xib, it is therefor the file's owner.
Other xib file are usually loaded through a delegate object. That delegate object is the file's owner. But the delegate itself is instantiated from code. It is not loaded from the xib. That's why it is not shown in Interface Builder.
xib files contain actual serialized objects. File's Owner and First Responder are exceptions. They represent some other, already existing object.
File's Owner (often a UIViewDelgate in non MainWindow.xib files) is the chicken. The xib is the egg. The chicken itself is not contained in the egg.
A bit long. Hope it helps.