While I agree that planets are in theory, occupied when you settle them.
The game mechanics disagree. The planets population becomes 0 at the end of a bombardment, and colonizing it starts the counter ticking with a minimal population.
I also agree that the developers have more pressing issues for Trinity and Rebellion, but as stated in my OP, this is an idea that could be implemented for an eventual true sequel, not in Rebellion.
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I just thought that culture could be used to sway a population, so that when you came to take the planet you could simply eliminate everything in orbit, then send a liberation force (Since they are of your own culture).
Conversely, without culture, an occupation force could be sent in to take the planet but maintain its current levels of population. Benefits would be reaped immediately but the planet would fall easier, grant less benefits and perhaps be easier swayed by enemy culture.
It would also allow for an interesting diplomatic tactic with the A.I. Liberate a planet occupied by a third enemy, but then give it back to the original owner for major diplomatic benefits.
Again, to re-iterate, this idea is meant for the developers, simply as an idea, for something that could be used as part of Sins of a Solar Empire 2; which will likely be in the works once Rebellion is out (At least, I hope so!).