I'd say your middle paragraph holds water, depending where you plan to build. If it's in established great house territory, you need to have it okayed from the great house. If it's not inhabited, you'll need to get it okayed from the duke or what have you that's incharge of land deeds (and if a place is sponsored by a house or not). Now, disputes do happen, because another house could be trying to encroach another house's territory. Such things usually handled through assassination, or just killing the people building the place and the owner.
But who would handle the territory for the houses, as I have a hard time seeing how for instance the Telvanni could have it owned collectivity, alternatively it is distributed to the masters or council members of the houses where it would be logical for them to own their own territory.
Assassination is one thing but how would the land deed and right pass over to the culprit, unless of course there is theft of the land deed involved, in which case where would it be stored?
Whenever you are going to build something apparently you have to go get a permit from the duke in ebonheart
Yes, but is this true for all territory or just the neutral ground? and is the duke the guy to turn to for all building permits or just that on his ground? and lastly does he hold all deeds or are there powerful free agents not bound by houses that could possibly hold large chunks of land?