Yes pl0x. Even on evenly spread galaxies like scattered, loose (which is a lot like scattered anyway), or spiral, the spacing is random no matter how much you play with the tall and wide values in the xml. Sometimes, they will be decently spread out, but more often than not, you will have one or two (or half of them) close together in one cluster.
Starting positions makes a HUGE difference in this game, and for the AI, it literally makes or breaks them.