TP,
I have read the article and I must say that it is well written and overall a very good concept that makes alot of sense. As you have expected, there are a few things I don't agree with, that being said, I do think it is a very viable program and people should see results.
Here are the points I disagree with:
You said that someone should expect to lose SOME muscle in the process, I don't think that you have to sacrifice muscle at all and in fact I have theory that many people gain muscle when leaning out.
I don't agree with the no carb day for two reasons, if it falls on a training day, you are not taking in any carbs which help replenish glycogen and start the recovery process, I realize the next day is a high carb but you would have missed that great post workout window of opportunity. The other reason is that most people will be weak and tired on those no carb days.
The last point is cardio, I personally hate it but it is very effecient at getting the metabolism cranked up and burning fat. Weight training is not effecient at this, it does build muscle which burns more fat all day long but cardio is a more effecient way to raise the metabolism and a good weapon in your fat fighting arsenal.
This is not a bash at all, like I said overall I think it is a good program.