There may be something in the flags, and without any further evidence I'd probably sign on to the theory that they're hamlets/villages.
As for the smallest text on the map, I'm 100% convinced it's deliberate gibberish. In the bottom right of the full map there is box with similarly sized text that is barely legible but still clearly Eorzean. If they could make that text recognizable, certainly they could have for the other map labels but they intentionally did not.