I’ve always yearned for something like this too. I wonder if, from the dev’s perspective, balancing the years and years such a thing would take in real time conflicts with other aspects of gameplay? Or maybe soil chemistry is too difficult a thing to gamify for a casual player (including myself in this- unfortunately I don’t grasp chemistry or physics easily).
A colony sim/resource management game in early access I played recently tries to touch on this actually- Farthest Frontier. As you might imagine from what I typed above, I’m heinously bad at grasping the system, but the building blocks are in there! None of the procgen ideas you’re interested in though.