I agree that the measurement method should have been changed to calories consumed and not those calculated based on heart rate... however, an interesting "experiment" just the same... at least as far as making an interesting article.
I would say that food consumption would be a better measure, but then you would have to subtract out some number of calories for normal metabolism... or maybe not, since it would honestly show the disadvantage of the cyclist, and that is that it consumes fuel whether moving or not.