As I understand it, any mission with objective: 3 will create a mission site wherever a UFO with objective: true decides to land. The mission should then be complete, and not spawn anymore waves. If other waves have already spawned before it lands, and they are also set to objective: true, they should also create a mission site wherever they land.
spawnZone: 3 will cause the mission site to be made at a random waypoint selected from missionZone: 3 which, by default, is pinpointed over cities. This gives a high likelihood of missions spawning in exactly the same place. Or perhaps the mission only ever selects one location for the site, and all UFOs belonging to the same mission which create sites land at the same position. I've never played around with it so I don't know.
You can bypass it by using multiple similar missionScripts to spawn multiple similar missions on the same month (in the same region if that's what you want) and have them make sites that aren't in the same place. Also, you can try using spawnZone: 1 or 2 which have large spawn boxes over regions, so that there are thousands of possible locations where they can spawn their mission.
