As Moose says they're mostly likely associated to Hamlets, small cities/townships. Places Roddard Ironheart would have stayed as he journeyed across Eorzea mapping the details. The odd thing for me is the detailed drawings of Ishgard, Gridania, Ul'dah and Limsa Lominsa and the vague copy/paste city design for Sharlayan and Ala Mhigo. Maybe he wasn't allowed into these cities for details or maybe a sting of the Autumn War still hung around Roddard so he gave preference to the 4 City-States.

The flags are at least grouped together...4 -> 3 -> 2 -> 2 -> 3...but as Moose stated the Blue Flag with the White Stripe looks to be associated it with Limsa or at least the ships near Limsa. So they aren't in order of the City-State, so I don't know the exact order, but a few places I think could be considered:

Ul'dah:
  • Golden Bazaar
  • Silver Bazaar
  • Camp Blackbrush --- This is where "outcast" and poor Ul'dahns live.

Limsa Lominsa:
  • Wineport
  • Aleport
  • The Cieldalaes --- Seems to be mostly fishing villages, I just include it in this list cause of the region.

Gridania:
  • Quarrymill
  • Hyrtsmill

Ishgard:
  • Owl's Nest
  • Eagle's Nest
  • Ferndale --- The town Nidhogg eventually destroyed.

Just a few examples I mostly wanted to toss in Fern(e)dale.