I'm not sure how it breaks out for air cargo (probably not great), but ocean and rail are both more efficient than trucks.
It's like saying cars produce less emissions than bikes by including the manufacturing costs of the bike but not the car.
How does the lamb get from the port to the grocery store? Is the port not roughly equidistant from the point of sale as the local farm? How is the “fancy organic farmers market” less efficient to ship to in the last mile before the point of sale?
That's not even mentioning the savings that can be had from home delivery. Although I had a local organic pig farmer deliver meat at home just yesterday, so that's not an advantage exclusive to large players (provided he has enough customers to do multiple drops on one tour - I should've asked him, come to think of it).