I first saw the article you linked on a day when I'd made hamburgers and salad for dinner, and it didn't pass the smell test. I calculated the cost per person of a whole-dinner-plate salad (made from fresh veggies, including bell peppers, cucumbers, and tomatoes, with dressing) to be about half the cost per person of a quarter pound burger. This was right after the Chile quake, which had doubled the price of some of those veggies.

A McDonalds salad costs more than a Big Mac, not because veggies cost more than meat, but because McDonalds salads typically come with meat (chicken/bacon) that's as expensive as ground beef, and the salad veggies, cheese, and dressing are more expensive than a hamburger bun and condiments. (The prices of non-meat salads are anchored to the prices of the meat-containing salads.)

I'm all for criticizing food subsidies, but let's do it honestly. Even with subsidies, ground beef costs about twice as much per pound as the veggies I commonly buy, and ground beef is at the bottom end of the meat spectrum. Subsidies don't make a Big Mac cheaper than a salad; price anchoring to chicken-bacon-ranch salads make McDonalds salads expensive.

You are forgetting about storage costs. Frozen ground beef, buns and condiments have a much longer shelf life than the typical salad ingredients.

One under-appreciated reason is storage. Frozen meat and most of the accoutrements can be stored for vastly longer and remain "fresh". Highly processed food products are all about preservation, to their nutritional detriment.