I was somewhat surprised by the outcome of the article so I emailed with Steve Guttenberg. He used a regular iPod Classic to a LOD. It wasn't an Apple to Apple comparison, more like an Apple iPod to "Orange" CLAS comparison. As John said, the source makes a huge difference. I've used by 3a with an iPod Touch with a Whiplash Reference Dock, which I would guess is better than anything Steve used, and it comes no where close to the Spdif input. As to why he didn't just go from CLAS>RX3>Fitear to CLAS>JH3A+JH16 is really simple. The 3A needs that proprietary connector to go from CLAS's coax out into the JH3A. There is no way Steve would have one.
Also, Steve has also clarified that he doesn't really consider the 3A and the Audeze 2 or 3 equal but different. He prefers the fullsize phones by clear margin. However, I still don't think he's ever really heard what the 3A can do. It performs at really different levels depending on how you are feeding it. The CLAS is nice as a source, but even that is significantly trumped by a laptop+audiophile software+high end transport (Halide, Audiophileo, etc.)+quality connector (Moon Audio). Once that chain is established, it really is phenomenal.
The CLAS>RX3>Fitear rig doesn't stress me out too much. Personally, I think the real challenge is going to come form the UM PP6.
Best of luck.