You can manually untangle a map by alt-right-clicking (IIRC) on the galaxy map and selecting a custom layout.
As for hidden untangling...I thought it untangled regardless of whether the map is hidden or not; you just don't see it happen. But I might, of course, be very wrong.
Well, I hit the button before I started and it didn't seem to work. As to manually untangling, I'm aware of that, but suffice it to say my latest realistic map is... somewhat intractable in that regard.
Edit: After some testing, untangling of hidden maps does indeed seem to work, I must have forgotten to hit it after the last "new map seed" hit. Oops. Still, it would be nice to be able to untangle after the game starts, for those instances when one forgets!