I like your Sauron and Dungeon Keeper analogies
Large scale games usually relax management of massive number of units by executing their individual logic less often when they’re out of player’s eye, like every second or more (especially for movements: it’s a lot more efficient to move a unit 60 meters every second than moving it 1 meter every frame at 60 Hz). It’s OK as long as it doesn’t make a significant difference and is not too noticeable by player. Still, what you describe looks like a bug (and not just bad tunings about it).
To partially respond to your last statement, there is this option in "Policy Settings" -> "Construction" -> "Prioritize State Ships in Docking Queues". Though I'm not sure if ships in construction count as "docked" ship, I'm pretty sure that already docked ships won't be expelled for your military ships.
kinda reminds of dungeon keeper where you could slap your minions from your evil dimension to make them work harder. they also seem oddly incompetent with refueling taking forever with none of their fuel gauges going up even though they're huddled around the spaceport. if the spaceport is busy making freighters i wish there was a way to make my military first priority. as if having space guns wouldn't do that anyway 
