Don't know about the science, but if you ask Bill Phillips he'll tell you there's more scientific research to back it up than anything else on earth... But then again, he says that about anything he recommends!
However, I have done the early morning cardio on an empty stomach for long periods of time, throughout the last 12 years and I've had great success with it. Not only are you forced to use stored fuel (because really, what else do you have when you haven't eaten in 8-10 hours?), but you'll find that you don't have to work nearly as hard to get your heart rate going at a good pace.
If you're really concerned about losing muscle, try drinking a pure whey protein shake, no carbs, no milk, just protein and water, before you do the cardio. The amino acids floating in your bloodstream should protect you from any meaningful muscle loss.