This started out as a question but I think I have figured out how to change a faction's starting status (from client state to neutral, for example).
1. Using EditSF, open up startpos.esf (make a backup before doing this).
2. Decide which 2 factions you want to edit and then find their faction value #s by going to compressed_data/campaign_env/campaign_model/world/faction_array/faction_array - #/faction. Their Array # will not match their faction number, their number is the first number listed when you click on FACTION. For example, Carthage is 3 and Libya is 85.
3. Expand the first faction's tree and find compressed_data/campaign_env/campaign_model/world/faction_array/faction_array - #/faction/diplomacy_manager/diplomacy_relationships_array. Then, find the value of the faction you want to edit the relationship with. For example, under Carthage's faction area find the diplomatic_relationships_array with value 85 for libya. Click diplomacy relationship and change client_state or protector to neutral.
4. Do the same thing for the other faction (in this example Libya), change that factions relationship to neutral for Carthage's diplomatic array entry (value 3).
5. Go to Libya's compressed_data/campaign_env/campaign_model/world/faction_array/faction_array - #/faction table and change the number following the word Carthage from 3 to 0.
Now, when you start a new campaign, Carthage and Libya should be neutral to one another.
I assume you can use this to make factions start as client states, etc. However, I haven't tested that aspect.