I can't agree with Shephard's methodology here. Why is he using RHCP to guide these comparisons? These are notoriously poorly mixed & mastered tracks - repeat offenders in the Loudness Wars debates that consume the audio engineering industry. Start with a record that is mastered to audiophile standards (say, RATM's debut) and then let's see if there's a difference. A piece of shit is going to sound like a piece of shit no matter what. Especially when the original (CD) master has digital clipping...
Further: "No differences" between CD and downloaded quality is a GOOD THING: The "Mastered for iTunse" AAC format is a compressed version of the audio data found on a CD (both are 16 bit, 44.1khz) so no discernible difference would mean that the encoding is transparent, does not result in a loss of dynamic range, and that the auditory masking effect does not leave artifacts.