The big difference I see between their two perspectives (they are both mentioning many of the same concepts) is that Lyle is trying to argue that Energy Balance still applies, that the calculation is just far more complex than what you typically see whereas Kiefer seems to be pretty much saying that thinking Energy In = Energy Out effectively is useless.
I have to wonder, how anyone could realistically apply an equation like
to achieve desired results... Even with all the resources and closest monitoring possible, you'd still be mostly guessing on a lot of these numbers, the average person certainly would have absolutely no use for a calculation like this when it comes to losing fat.
The equation becomes useless, even for the most controlled, monitored athlete, nobody could ever apply it and I personally don't think anyone needs to give it a huge amount of consideration when they want to lose body fat. There are more important factors, macronutrient ratios make the biggest difference for me when it comes to how much body fat I'm carrying, not the sheer number of calories ingested.
3000 calories from Protein and Fat are metabolized very differently from 3000 calories of sugar, or even 2000 calories of Protein/Fat and 1000 calories of sugar.