Calories vs. % Fat Burned

Exactly! Furthermore even if respiratory exchange ratio (RER) is lab tested, still it is VERY hard to conclude what type of fuel your body is relying more since all this can be affected based on intensity, duration of session, fitness level, genetics, diet, environment, etc. It is not only meaningless to track this using something such as a HRM but I also find disconcerting to know that some 'coaches' test their athletes to establish what fuel the athlete relies on when exercising to determine their training *sigh*

During the exercise you mainly burn carbohydrates (glycogen, glucose...), fat and proteins. When you train at a lower intensity the body normally burns mostly fat, when you train at a higher intensity your body starts to burn more glygogen.
However, the burnt glycogen needs to be replaced and the energy you loose for this is equally as beneficial for you fat percentage.

So, it doesn't realy matter how much % of the burnt calories directly comes from burnt fat. So, it's all about the calories themselves.
When you run exactly the same time with a hihger intensity you'll always loose more fat as a result of that training. When you run a longer time with exactly the same intensity you'll always loose more fat as a result of that training.