🔹The problem with the Genesis series is that the mod uses all the good locations to build new cities (and removes a little of the desolate land aspect intended by the game) There is no room left for the player to build his own bases. That's why I describe this collection as a Vanilla+ experience, rather than a total overhaul.
🔹About the multiple cities, I think it's a conflict with another mod outside of this collection that adds elements to the cities. Many are not compatible with each other.

Almost all of this collection is included in Kenshi Genesis Megamod v9

multiple versions of cities are overlapping therefore making it impossible to enter or exit

Gonna give it a try!