For example in this study did they consider the food usage of someone sitting on a bus or driving a car in their study - I would guess not.

There's been a lot of hemming and hawing about how biking or walking might not be so eco-friendly because your body burns more calories during those activities than while driving. But, frankly, that's bunk: As the Pacific Institute has shown, you'd have to be eating an all-beef diet to offset the environmental benefits of walking or bicycling. Given a "typical U.S. diet," you would have to ride your bike instead of driving for around 400 miles to cover the bike's initial carbon footprint.