It's for the AI expansion script.
The AI gets free settlements to make up for being, well, the AI. Players are way smarter than the AI at the moment, so the only way for the AI to keep up is to get special bonuses.
The AI gets free money every time it goes bankrupt.
The AI gets free settlements at the start of the game.
The AI gets free armies when it starts to lose.
The AI gets a population growth bonus.
The reason why these cities are empty is because the AI gets a free army next to the cities so they instantly have that city without needing to fight.
The light regions are the regions the AI gets for free.