"Naturally, these higher psuedo-dimensions, while similar to Einsteian or Cartesian space, have a few distinctions. Most obviously, while three dimensional volumetric objects can exist in them, real-space three-dimensional maps, when projected into "hyper-space" appear to be two-dimensional. The fact that they allow faster than light travel is merely a practical application of this fascinating theory. "
So yeah, you could simply rearrange a real space map onto a 2D area with some kind of algorithm based on the real distance to the star; a star that is above the orbital or galactic plane but close might end up being adjacent to a star that's below the galactic plane but just as close to Sol. . . but that's just the "mysteries of Hyperspace" for you.
Now, that all said, a random galaxy map would be interesting and allow for a lot of control over the generator. I'd say that on balance, I'd rather have the random galaxy with controls, but there's no reason why having a premade "real" galaxy map wouldn't work- or even having a galaxy construction set for other premade galaxies.