Surely in todays world, it's very cheap to simply have a bunch of cameras looking down at the plants, and track from each seed, to each plant, to each leaf on the plants, to how many cents that plant earned you.
When you have that kind of tracking, you can do things like "If a plant is within 30mm of a neighbour, we will earn more if we kill one plant and let the other grow. Kill whichever is currently smaller".
Or "if a plant is growing within 2 inches of a rock, give it these extra nutrients".
Treating each plant separately should give much higher yields.
Our current system is equivalent to a human medical system which doesn't inspect each patient individually, but instead just prescribes medications to entire towns!