If such a system really gets added to the game, I don’t feel like free-form base building like Ark or Fallout 4 would be the best solution, so here’s how I’d do it:
I would create a system that’s similiar to a mix of Far Cry and Mad Max/State of Decay.
There would be certain locations, for example Masskar Resistance or Saltholmen Naval Base, that you’d have to clear of enemies. Then, the resistance/military/police/Iron Church/whoever would move in and secure the place.
Now you could start building.
Avalanche could just copy the system from their Mad Max game. In this game, each major stronghold had some unfinished building projects, for example a water collector, that, once finished, would refill your water flask once a day. In GZ this could for example be a medical post that generates a few medical supplies per day, a kitchen that gives you a buff once a day, or an artillery piece that allows you to call in fire support, etc…
If they really wanted to, they could also do what State of Decay did, and give each base a few empty slots, where you can pick a building from a list.
I’m not sure whether or not NPCs and base building would fit into the game, but if they were added, that’s how I personally would like it the most.