Question regarding the map of Eorzea

[Anonymoose]

[W]hat about those below?

I wouldn't discount the smaller symbols as being cities/townships. The "big four" there are the official members of the Eorzean Alliance, which was originally founded to combat the over-bearing military might of Ala Mhigo. That would explain why those four take prominence in the design, both in detail of the city-states on the map as well as the larger flags. The first version of this map was drafted in 1506 Sixth Astral Era, so perhaps that timing lines up.

The blue/white one is familiar but I can't quite place it yet...

Based on the grouping of the Eorzean Alliance members, I think it's also safe to assume the others are grouped according to some relation. What can we make of those groupings?