The best part about this is when you take over a synthetic planet and the robots start having babies.

Or synthetics take over a planet with billions of meatbags and insta-convert them into synthetics,   yet building another single pop's worth of synthetics takes their homeworld months.

(Missed opportunity:  researchable tech that would allow for insta-conversion on conquering a meatbag planet,  with percentages and converstion rates getting better with more levels.. I dunno.  )

Lots of room for improvement here. 

I don't think what OP mentioned can be called ludonarrative dissonance because the game doesn't give a narrative for what is happening. I think it's a missed opportunity because there could be a lot of mechanics involved in the situation that OP described. Perhaps the citizens could be transferred after the war in a pow exchange, or perhaps if they stayed in the new empire they could contacted by their former government and secretly become spies for their former faction.

I also agree with OP that it adds to the snowballing effect that most 4x games have. You never really have to deal with "imperial overstretch", you have the commonwealths but your space empire never really falls appart on itself. The focus in GalCiv III and 4x games in general is too much on warfare I think, sure everyone and myself included like the cool explosions but the context to why it is happening is made mostly by the player. This context usually is that you just have the ability to do so. And the result of a war is usually eXpanding or eXtermination and also helps getting the other victory conditions. The problem here is that wars are too predictable, there is little risk or unexpected situations involved. You can see when you have an advantage and safely conclude that you will win. I find the early wars always to be the most fun because you have to manouver far more carefully both diplomatically and militarily because those battles in 4x's are usualy uphill. When the late game comes and the ai's all hate you because of your advantage they all respond too late because you already consolidated your lead.

I made a really long post about this in an old thread so I'll try to not make it too long. I believe I mentioned The Mediterranean (and the Mediterranean World in the Age of Phillip II) by Braudel. In short it's an analyses of the famous sea battle of Lepanto of 1571, traditionally (+-100 years ago) historians saw this as the battle that resulted in Spanish domination of the seas. Braudel shows that the actual result was a reaffirmation of the status quo, the Ottomans had rebuilt their fleet in the years after and still dominated the eastern mediterranean like they did before. But far more importantly the lives of people arround the mediterranean didn't really change, life and trade went on and piracy was still a big concern for example. Braudels conclusion was that history moves at different speeds. The surface layer or scale is what is most clearly visible it is the "short" term political events like elections, trade deals, (civil)wars. Beneath that we have the economy moving at a slower pace in buisness cycles or seasons. And finally beneath that there is the geological scale moving so slowly we don't even notice it (except for maybe the Suez canal in this case). All these different scales interact and shape the "stage" in wich everything is happening. Now what does this mean for  strategy games and maybe for GalCiv III? 

• Geography: The game map needs to be interesting the entire game, the growing ship ranges already slowly open the map during the game and the hyper gates changing the geography but there could be other ways. The planets in the game are quite unique but the star systems are far more alike. There could be different sizes in stars with vast red or blue giants that slowly damage ships' shields or armour when they fly to close. Maybe a star could go supernova like in MOO. There could also be different sizes for all the other celestial bodies in the game like the black holes for example. I remember a promotion image of the game with a human fleet in what seems a path through nebulae and asteriods, this could be an important trade route on the map in a skirmish game. Some nebula could perhaps completely block all sensors (Drengin surprise attack, anyone?). Or maybe some nebula could be damaging shields until you discover some hidden tech developed by a scientist/citizen working near that region (and the ensuing Drengin surprise attack of course). Or maybe fleets could hide in the upper layers of gas giants. Terrafroming could be made more interesting more on that in the next section. 
• Economy: The development of planets and the economy would be the eb and flow wich partly steers everyones plans because of price fluctuations for example. The player has a lot of control over the economy I think it might be more fun if it could feel a bit like it's an entity on it's own. Perhaps trade routes would form on their own between populous planets and production centra. Which planets become important trade hubs could be facilitated by signing treaties or building ever bigger space ports in your trade hub systems , clearing a path throug nebula/asteriods, build a hypergate connection with another trade hub. Wars and changing geography could in turn shift were the important trade nodes will be changing the economic situation for everyone. What if A minor race planet is a major trade hub in that part of the galaxy, attacking it for example could send everyones economy into chaos because of the disruption trade. For terraforming and long term economic plans I think MOO has the best idea. Every type of planet could have it's qualities and those could slowly be opened up during the game. Instead of the extreme colonization tech threre could be techs in the tree that also benefit terraforming, like the planetary shield that helps terraforming radiated worlds in MOO. Volcanic planets or moons would be ideal places for some industrial processes that require a lot of heat.
• Political events/player and ai actions: All layers should interact with eachother but this will be the most visible one. I think 4x games could be a lot more interesting if choosing war was always a risky move. Invading planets could also be something that is slowly built over the course of a game. Maybe raids is the best you can technologically do until the mid game. If ground battles would take multiple turns perhaps you could send your legions down to temporarily capture a research facility and maybe get that important tech before pulling out. Ground and space combat could be linked too. If your legions capture a ground to space cannon it would give a advantage in nearby space battles. Perhaps different ground units like tanks, mechs and artillery all with their preferred terrain and combined arms bonusses would make invading different planets more challenging.

I'm going to end here because it's getting too long. The most fun I had with strategy games were the times when unexpected things happened, my actions had unforseen consequences or fighting an uphill battle. In most 4x games the challenge dissapears when you start to snowball. This is perhaps more true for space 4x games since victory conditions are a bit more intertwined then in Civ for example. The context of the actions and decisions you make give meaning to what is happening this also goes for strategy games. It is or could be more than that one specific map or that one unlucky decision that set in motion a series of unfortunate events. When the game world responds profoundly and logically to these changes on all levels it will make random skirmish games even more memorable.

I'd say the game design reason is simple:  it was easier to code.  They didn't want to spend time on it.

The spies was just an example of maybe mixing up the existing game mechanics. It wouldn't make sense to attribute it to certain types of citizens because then you would exactly know who to trust and who you can't trust, in multiplayer that would defeat the whole purpose. It also isn't entirely a question of GalCiv being immersive or not but one of game mechanics interacting that generate a game world were you have to make strategic choices. I haven't played Civ 6 but the latest expansion with the global warming mechanics that change the game world and force you to make new strategic choices in the end game seem really interesting for example. GalCiv is never going to be realistic and it doesn't need to be but it can be it's own universe with it's own rules, the 2d map could be a lot more interesting for example.

As for immersion just for immersion's sake I think this is still somewhat important for any game, look at the popularity of Stellaris. It has a ton of flavour text that creates immersion for your empire, compare that with the word on the street on the planet screen in GalCiv II or III. I don't think a Drengin would value the same things on his home world then a human for example. But for a strategy game, strategy and intersting mechanics should always come first. I wouldn't play Stellaris for the strategy aspect, because the ai is incapable of playing the game making some game mechanics just a facade that doesn't involve any strategy. For GalCiv immersion was considered important enough to include a campaign which I don't think it needs when the mechanics are nuanced enough to make the narrative for you. For example in Endless Space 2 the political landscape in your empire is slightly changed by almost every decision you take, like what techs you choose, what buildings you build, etc.

GC3GlobalDefs.xml - Will be in you newest expansion folder.

AbilityDefs.xml - If you want to tie it into an ability or abilities.

That will be interesting to try. The problem I see is that I doubt synthetics will be able to supply food for conquered meatbags, simply because they can't build farms. However, I see no logical reason why the conquered pop couldn't build farms and grow food for themselves.

I got it working... you can do two actions in the one event wrapper, so good.

Although it's depressing because once I start hard core modding a game... I never really play it again. Spend 90% time modding, and designing new things, 10% playing the results... agh. I will not succumb here... because GC3 is actually a working good game, unlike the other one I won't mention that ended up modding to hell and back with results? It's still a stinking pile of...