Sounds like a fundamental problem with the organic product, on top of the existing lower expected calorie yield per acre.

If you actually want to optimize calories per unit land, you should be considering neither organic nor non-organic tomatoes, as both produce significantly fewer calories per unit land than crops like wheat, corn, and soybeans.

Or any kind of product other than plants producing edible oil. Maybe lentils and soy and wheat.

I'd imagine the honor of "most efficient yield" would belong to root vegetables like sugar beets, yams or potatoes

I believe it does, particularly if you use techniques like potato boxes (I haven't tried these yet so not sure how effective they are.)