It looks like the procedural generation is used for many aspects of the game (what zones are void for example) but otherwise factions and zones are serialized and authoritative. Messing with the easy to parse xml zone summaries only changes what showed up on the map :'(
If I can figure out the zone and faction marshaling format I would be interested in building tools to generate/customize galaxy maps for servers.
I expect the marshaling is a common format, but I did not recognize it on sight. Can any members or dev(s?) identify it?