I think when organizations have a certain territory locked down they'll want to rent out land (or buildings/hangars) to make money.
It would be in their interest to have services like markets and such to incentivise people to live there. If I was a miner I'd rather rent a hangar to store my stuff and ship and have the org take care of the security.
If a organization is successful in making money from a city from rent and taxes then other organizations will fall suit and compete. I think the leasing and selling of secure land will be a key driver in cities appearing and I'm sure the devs have other ideas to create incentives to make cities appear naturally.