This command is tricky, if cycrow hasn't pointed me to it i'd still think this flag had no real usage.
The sector map is deceptive on that matter (and many others), ships with this tag are created "on the fly" when it's opened according to the "max ship per sector" (or something like that) flag. However when you check the job list in the script editor you only see around 20 "job.stationtostation" instead of the supposedly 200.
So, they are generated when the player open the map and when he enters a sector with civilians inside. I'm not really sure if it occurs when you use one of your ships to jump in the oos sector, it would make sense as you can target/attack them from OOS, but it raises a few questions like: "what happens if i orders my M6 to attack a civilian i see on the map OOS, and then close the map before the M6 reach the sector?".
And whatever the answer is, it of course needs calculations from the engine that could be put on a better use elsewhere. I'll probably investigate on that matter anyway as i'm really wondering how all of this really work. I'll post results if anything interesting happen.
Fortunately it changes little, since even if it did work it could still only be applied to "ornamental" flights that give flavor to the universe, and have no real purpose. Removing something like a Pirate, Yaki, or Khaak from any sectors that qualify as OOS, would mean visiting ships would have no interaction with them, as they wouldn't exist.
For pirates and yakis you're right, moreover their job is supposed to make them move from a sector to another, and i don't think the engine will like that mixed with the OOS tag. However, for the khaaks, who run a simple attack.all script, being able to remove all of them when OOS could be beneficial, at least if they start existing when a player owned ship jumps in.