Actually you can, and I already did some of that. In worldbuilder, you go to edit player mode, right arrow, territory, and click on the player name of the city you want to give it to and click the city.You can't change the ownership of a city in the worldbuilder
BeginTeam
TeamID=16
ContactWithTeam=16
RevealMap=0
EndTeam
BeginPlayer
Team=16
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
RandomStartLocation=true
EndPlayer
BeginTeam
TeamID=16
Tech=TECH_MYSTICISM
Tech=TECH_HUNTING
ContactWithTeam=16
RevealMap=0
EndTeam
BeginPlayer
Team=16
LeaderType=LEADER_BOUDICA
LeaderName=Boudicca
CivDesc=TXT_KEY_CIV_CELT_DESC
CivShortDesc=TXT_KEY_CIV_CELT_SHORT_DESC
CivAdjective=TXT_KEY_CIV_CELT_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDECAL_CelticCross.dds
WhiteFlag=0
CivType=CIVILIZATION_CELT
Color=PLAYERCOLOR_LIGHT_ORANGE
ArtStyle=ARTSTYLE_EUROPEAN
PlayableCiv=1
MinorNationStatus=0
StartingGold=0
StartingX=43, StartingY=4
StateReligion=
StartingEra=ERA_ANCIENT
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_DESPOTISM
CivicOption=CIVICOPTION_LEGAL, Civic=CIVIC_BARBARISM
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_TRIBALISM
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_DECENTRALIZATION
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_PAGANISM
Handicap=HANDICAP_NOBLE
EndPlayer
BeginCity
CityOwner=12
CityName=Chichen Itza
CityPopulation=2
CityCulture=10
EndCity
I got there, but I seem to need to add all of the cities for the civ.
I also apparently have 17 civs, not 16.