With the modifications, it seems that the Mutants and Vault Dwellers don't come into conflict anymore.
This may be an unintended consequence of limiting the Vault Dwellers to one vault per civilization. Now, the Vault Dwellers and Mutants don't ever seem to meet one another, so they can't learn to hate one another.
While this may seem pretty accurate according to the Fallout games, it isn't really as much fun.
Perhaps there's a way for either the Mutants to seek out the Vault Dwellers, or for the Vault Dwellers to attempt limited expansion, like in Fallout: Tactics.
In the Fallout game, the chief problem that keeps the Vault Dwellers from expanding is their limited numbers. Generally, there are only enough Vault Dwellers to keep the Vault at a constant population. So, there are no extra people for expansion. Perhaps limiting the population of the Vault Dweller civilizations can make expansion difficult, but possible.
Of course, once the Enclave is added to the game, things will get more interesting. I'm flashing back to the starting sequence of Fallout 2. Brutal.
Ok, I just tweaked some things, and the results are interesting. First, I extended the starting year from 100 to 200. Second, I increased the starting civilizations from 20 to 25. Usually, extending the starting civilizations can cause near-infinite rejects, but in this case the starting civilizations and map features are such that it turned out ok. I get into the game, peek at the legends, and find out that the mutants have been waging a rather lengthy war with one of the vaults! Unfortunately, they declared peace, but it's progress!
Also, I noticed that the Ghouls have "desert_badlands" set as their starting biome. If that were set to just "desert" they would have a far greater chance of showing up on the map. "Desert_badlands" seems like a high savagery biome, and high savagery can heavily prevent civilizations from forming.