There's a few solid points in the author's understanding of exercise physiology, but as compudog points out, he's getting confused at some things. I'm only hitting a couple of the bigger things, but,
The "fuel continuum" he's talking about is true only to a certain extent. Unless you're doing fairly low intensity workouts all the time or your body is condition to use the fat oxidation cycle more (high endurance athletes) carbohydrates are almost always relied on primarily. Whenever you work out, your RER values shoot up. The RER values range from 0.7 (fat use) to 1.0 (carbohydrate use). It can be greater than 1.0, but that's due to buffering on your H+ ions.
Additionally, HIIT isn't effective because of it's "greater dependence on carbohydrates", it's effective because it allows you to work at a higher intensity for a longer period of time by having rest intervals. It burns more energy after the workout has ended due to more muscle fiber repairs it has to do as well as the accumulated oxygen deficit it's built up.
Another point includes the thermogenic effect of food. Yes, food does have a thermogenic effect. The problem is, your body doesn't digest much food while you're working out. The majority of your blood from your digestive organs are diverted to your skeletal muscles to provide more oxygen.
Breakfast, as more and more people are starting to know, isn't as important as it once was thought. I do love eggs though.
One important thing people need to remember out of this article though, is that you do start to breakdown muscle as a fuel when your body isn't fed and isn't able to keep up with the energy demands. (Berkhan suggests having some BCAA's before this to get around this problem).