Wow, OK, a lot has been happening here.
The dark ores issue might be Iris rather than Sodium.
AutoFarm not spreading crops to blank farmland is intentional, since there are many different types of crops it could plant there and I don't want it to mess up people's farms by planting the wrong type.
Let me see if I can figure out that TreeBot bug... Oh that is super weird. It placed the stem marker in the wrong spot and completely messed up how it parsed that tree. How is that even possible?