Yep, if you look closely at what he eats (I don’t believe he has released his food logs), he eats way more than just a meal. There are numerous other items around him he is eating. Claimed 5,000 calories a day, but Big Mac meal is less than 1500. So he overstuffed himself.
As I recall, in the movie he did provide a segment in which he interviewed a guy who ate nothing but McDonald's menu items and maintained a HEALTHY weight and had no other health issues. This man practiced moderation and suffered no harm.
I don’t go to McDonalds often but when I do, it’s usually an Egg McMuffin and a cup of black coffee - 300 calories. The documentary maker was basically a jerk. I mean, in general, McDonalds is not the healthiest place to eat everyday - everybody knows that. But you could go into a Whole Foods and gain a bunch of weight too if all you choose is the fattiest items and “super-size” them.