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.

something like this integrated with space exploration would be super cool as well. im thinking: you can travel to different planets and collect plants from them and they have different genetic traits that you can bring back to your farm and crossbreed them with your plants with a somewhat accurate replication of mendelian and non-mendelian genetics. or maybe this is just my own fantasy as a biologist lmao.