Came here to say exactly this, glad someone else had the same memory of that game that I did! You should check out a game called "From Dust", it's made by the same designer but much more recently, the creatures and the world have a similar look: https://www.ubisoft.com/en-US/game/from-dust/
Admittedly probably pretty far from base building but I really like
From Dust https://www.ubisoft.com/en-us/game/from-dust non controllable npc build their village and you change the environment to help them out
And
Far cry primal the base/ community built itself as you progress through the game.