I noticed that in the Space Opera setting that the various polities (see Star Sector Atlases) are generally separated by large distances with undefined areas between them. But within any given polity one can find systems that are aligned with other polities far away. Space Opera polities tend to be federations, so this doesn't seem to be a huge administrative problem. In the case of aggressive empires, these systems are usually toeholds for an eventual invasion. Have you designed a setting like this?