How about some investigative journalism?
I find the article quite limited in scope, frankly. All the theoretical postulates can be argued about as much as you like (and I find some missing even from the comments). The empirical part seems to be inhibited by the particular procedure of ripping to a lossless format on a Mac (no criticism of Apple intended). Chris, how about you do some empirical research that goes beyond your own set of speakers and your own Mac and report on the results? Let's devise a few experiments you can do as a journalist.
1. Have you got an audiophile friend with high end equipment? Rip the CDs to FLAC and MP3 and listen to the originals and copies on his equipment and see if you can tell the difference. Intuitively, low end equipment has a bias in favour of lower quality codecs, so high end equipment makes a better experiment in this sense. Whether you can or cannot hear the difference, that will not tell you much about the reasons why, so move to the next phase.
2. Find a decent, professionally staffed audio equipment store and tell them you would like to get a reasonably good, better than basic consumer level shit, but not outrageously expensive audio setup. In my experience, what they will do (after some general questions and a discussion of what you are looking for, budget limitations, etc.) is invite you back with your own CDs. Ask your audiophile friend to help you pick a couple of CDs that are not completely lousy to begin with, and also bring a CD with FLAC and MP3 of the same music - ripped from the same original CDs - on it. They will line up a few decent receivers and a few sets of speakers and will start switching between them while playing the same tracks. My guesses are (assuming your audio perception is not completely degenerate): a) the same digitally recorded music played on different equipment combinations will sound completely different; b) some combinations - not necessarily the more expensive ones - will sound rich in texture and great overall while others will sound flat and poor. That's with the original CDs, no lossy codecs or anything.
[Disclaimer: This item is based on my own experiences choosing audio equipment. YMMV.]
3. Tell the store guys that you do listen to downloaded music and not just to original CDs and you would like to test how the various combinations handle that. Chances are that their DVD player will handle the formats natively. Try to listen to FLAC and MP3 on those combos that sounded great and on those combos that sounded poor. See if you hear the differences in either case.
4. If you can, bring your audiophile friend along for the experiment ("to help you make a choice") as well, as his ears are probably better trained. Don't worry if he likes a different receiver/speaker combination - this does not mean you have a hole in your head, it is very individual. The point is, whether or not he tells you that he hears a difference where you don't, it will be significant.
Report here. The results of the experiments above cannot be published in a peer reviewed journal (small sample, no objective measurements), but will be quite suitable for El Reg, IMHO.