I was thinking, maybe there should be an exclusion zone around a homeworld. Maybe 1 or 2 jump radius where no other NPR homeworlds are found.
What might be easier, and would also avoid allowing players to expand slowly in the knowledge they are perfectly safe, would be an amount of time at the start of the game during which no alien races would be created. Although in v4.0, at least one NPR starts at the same time as you in an unconnected system, so they will be building up too.
Steve