Thanks for the insight. It's interesting why the external work supplied to the plants still costs less than growing plants that can do these things itself. I suppose chemistry and mechanization in agriculture are just much more efficient than their biological counterparts.
Using externally supplied fossil-fuel is kind of cheating. The energy still comes from photosynthesis, but the energy that was created over eons is used in (geological) moments.
It's somehow similar venture capital. It's a resource produced in older times that allows you to get temporary advantage compared to somebody that uses just in-time generated resources.
Almost certainly not more efficient, but growing plants can't use oil directly, and since we can supply enormous amounts of external energy by the standards of a crop plant, engineering them to be able to use it more effectively is useful even if the plant itself is less efficient overall.
Almost any sort of mechanical or chemical process is more efficient than plants. Photosynthesis is only 3% efficient; by the time the energy enters the plant, you've lost 97% of it. Then you figure various biological pathways, and you're down to maybe 1-2% efficiency for the best plants.
This, among other reasons, is why grain ethanol was such a scam.
The worst mechanical processes, by contrast, usually get at least 10-15% efficiency. That's what photovoltaics can do, for example. Gasoline engines have a thermal efficiency of about 30%, diesel about 45%. Granted, you lose energy in the extraction/refining/transportation steps, but it's still an order of magnitude more efficient than photosynthesis.
The primary [photosynthetic] reactions have close to 100% quantum efficiency (i.e., one quantum of light leads to one electron transfer); and under most ideal conditions, the overall energy efficiency can reach 35%. Due to losses at all steps in biochemistry, one has been able to get only about 1 to 2% energy efficiency in most crop plants. Sugarcane is an exception as it can have almost 8% efficiency.
Not sure if energy is important part of the equation. Protection from diseases and weather doesn't seem to require energy, it's about chemistry and structure.