Hm, sounds difficult...but I'm not a modder anyway.

The CAMPAIGN_SCRIPT.TXT has a section for each faction which list all cities with the precursor building (homeland = lvl1, expansion = lvl2, outlying = lvl3+4).
I've just tweaked it a bit to get a lvl2 instead of 3 in some regions, but I have no idea if that works with the eleutheroi faction. The eleutheroi faction is divided into some subfactions, that have equivalents in the playable factions and can probably build the same gouvernments as their equivalents...or so think.