During Brad's work for the 1.9 update, he moved the pirates further away from the starting locations of the Races. This reduced the locations where they can appear, so they tend to group together in smaller areas. I have seen 9 pirate bases in a small area.
If you play with tight or loose clusters, some pirates show up in the empty spaces, but I have not seen a large number together in the empty spaces.
For all the star distribution options, more Races will result in less room that is far enough away from the starting locations, so the fewer pirates you will have, even on abundant pirates. If you reduce the number of Races, you will find a lot of clusters of pirates.
As you mentioned, the random number generator will adjust things also.