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You forgot about the height. It will overshadow the smaller crop, and lack of sunlight on this smaller crop may simply not produce any ears as a result. Just a "balcony farmer" but that is what i have seen with most plants that are overshadowed by dense/taller plants.
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A good story that touches on this is the Wizard and the Prophet, covering Norman Borlaug's efforts to crossbreed wheat that wasn't too tall, was resistant to blight, etc.
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That reminds me, I never got back my copy of that book...
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That’s true in generation 1, but breeding isn’t a single generation. You repeat things across generations until you find a stable mix.
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You just raise the head.

You harvest the top crop, the one you want, cutting above the lower height, then go back through and make a second pass with the head lower.

You'll lose some of the lower crop, crushed under the wheels, but it was there as bonus anyway.

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