No society that believes that space is 2 dimensional can really be thought of as enlightened. Most of the imperium is the TL15 version of the flat earthers.
Jumpspace is a 2-dimensional plane that roughly maps to the location of stars in our universe. Since the only important facotr in planning jumps this the coordinates on the flat topogrophy of jumpsapce, maps used by travelers ignore the realspace position in favor of the more usful map. Much in the way that railroad maps ignore irrelevant terrain features as they can't interact with them.
Today's lesson brought to you by Handwavium.
If you really want to use a 3d map with a Cartesian coordinate system, go for it. But understand that it changes the game radically. There are an estimated 14,600 stars within 30 parsecs of Sol. if they were all settled, you could cross human space at Jump-2 in about 4 months. A far cry from the "remote government" mentioned in Mercenary.
Expanding the sphere only makes things worse. you are very quickly into the realm of millions of star systems.
One thing 2300AD got right was setting it as Earth was just starting to seriously colonize and explore. This limites the size of map and the number of worlds easily accessable.