For the sake of performance, I would handle it the way they did it in Jump to light speed. One seamless universe would be amazing and you could do it using streaming levels or world composer, but I would just fake it using level switching. You could have multiple levels created each with their own space box, atmospheres or even transition to planets.
What we did for our game was created multiple map layouts and then called the those maps in an array and it would randomly choose which layout to load into. This is a little harder with streaming because you have to make sure that the levels meet up properly at entry points.
Anyway for each of those levels you could have a string or name variable set that represents a coordinate system, but in reality it just masks the levels name. So when you call a map switch it would look like its calling that map from a set of coordinates which would then fire off a canned loading screen that would look like hyperspace or something.
Multiplayer on the other hand would have to be handled a little differently. But going this route would allow you to have servers running multiple maps at a time (taking into mind resource requirements per) that instead of just a map switch it actually connects you to a different server/map.