What are your Goals?
Long marathons can cause muscle catabolism because of the need for energy but this only happens in long marathons.
I think your PT wants to increase your metabolism for a longer period of time. This helps with fat loss and muscle anabolism depending on your nutrition. To be honest I prefer intervals but you can integrate cardio on your off days as long as you have a good pre and post workout nutrition (basically high carb, mid protein, low fat, for Pre-workout and high carb, high protein, low saturated, fat high healthy fats for post workout), is not a lot (not more than one hour) and you get a lot of rest.
Sometimes intervals are just more convenient because you get more fat burning effect for a shorter session. You could also do some longer intervals, not as hard but you are still going as fast as you can for a longer distance or period of time. At the end, the winner is the one who gets there first.
I put this as simple as I can explain it without opening a book
Hope this helps
Rick_CSCS
ttfatlossworkout.com
Low Intensity Exercise = (LIE)