From the OP link:
The researchers conducted a meta-analysis of life-cycle assessments quantifying the water, energy use and emissions for more than 100 foods. They found fruits have the largest water and energy footprint per calorie. Meat and seafood have the highest greenhouse gas emissions per calorie.
To create a baseline of how many calories the average adult American consumes, the researchers used weight data provided by the Centers for Disease Control and Prevention and calculated how many calories a person would need to consume in order to maintain that weight. The average calories per day came in at 2,390 per day, or about 200 more than recommended. The researchers tacked on an additional 1,230 calories to account for food waste.
"If what your concern is the greenhouse gas emissions or energy or water use of the entire system, I don't think you should leave out large chunks of it," Fischbeck said. "If you want to know how much energy is being consumed, you have to include waste and what is lost from grocery store or dining room table."
That's not to say all vegetables are bad. Onions, okra, carrots, broccoli and Brussels sprouts all have decent environmental footprints. Lettuce, on the other hand, is difficult to grow, harvest and transport. It requires significant amounts of water and energy to produce.
"I would eat less lettuce and more Brussels sprouts," he added.
This would seem contrary to your accusation that they're not counting the impact of the whole pig. They are accounting for waste, for starters. And compare this to fruit and nut trees. We don't compare the food with the mass of entire tree.