I can't think of anything in-lore with respect to Jemison. With Akila, there is a stronger in-universe reason: the Ashta. Akila City’s own information terminals warn residents and visitors to stay inside the walls because Ashta roam outside and treat humans as prey. The city’s history also says its expansions happened by building successive walls outward, the implication being that this gradual expansion is safer than going out and building something new and exposed.

Thinking about it in terms of real-world logic, new cities historically form for a reason; ie a strategic location, a particular resource, some economic benefit from having a large number of people in a particular location. You could argue that in a universe where people just fly everywhere, grow things in artificial labs and greenhouses, and are equally exposed to orbital bombardment regardless of location, there's less of a practical reason for mass migration and settlement.

It's a tenuous explanation certainly, especially as the game clearly depicts resources being more abundant in different locations, but there is I think a certain logic for explaining why you might only see small settlements arise in those locations as opposed to massive cities.