Hi Tim,
Good post. What is a good reference system? A good question. Basically one that you have by which you judge all others that you hear, and that compares closest to a live performance. Usually it will have all components separate for the sake of flexability (ie: changing/tweeking DAC, phono stage, interconnects, etc, etc.) which you don't have with the all in ones.
Done right, with proper component choice, cable matching, and room acoustics, a "reference" type system is likely to trounce a system based on one of these usually very affordable all in one amps. When you say "your mileage may vary" you are totally correct, because taste IS involved.
I hope my post was not misunderstood as being down on all in ones - far from it - I've recommended quite a few on here. Case in point: a customer bought some Super 3is from me and played them on his expensive MacIntosh front end. He then got a PS Audio sprout and liked it better with those speakers than with the Mac gear. In other posts I have raved over how good the Audio Engine N22 amp/D1 DAC combo sounded with Super 3is, and that rig is likely lower on the food chain than a NAD 3020D, PS Audio Sprout, etc.
Here is the advantage of the all in one amps: 1) all the internal components are matched to each other. 2) less cables to buy, not to mention connection length between internal components is almost zero. 3) very aesthetically pleasing, compact, and easy to install. 4) sound value for dollar is very high. Roscoe mentioned some of the downside so I will leave that alone.
That said, take one of the pricier all in ones like the Wyred for sound mINT @ reg $1500 (on sale right now at $1099) and compare it to a very compact "separates" front end like a basic Decware Super Zen amp, Resonessence Labs Herus+ USB DAC, and one of the great little phono stages out there for around $400, and go with very basic cabling. Yes 25%+ more money, but the core of what I would term an entry level reference system with incredible flexibility, yet very compact. The Super Zen has two inputs, bias switch to change the sound, and many different brands of tubes can be used to tailor its sound. The Herus+ DAC/headphone amp/preamp will work with a computer, iPod, iPad, iPhone, Android using the portables power, it also has low power mode, user selectable upsampling filters, plays 16/44 to DXD. It's a fabulous headphone amp and will drive some of the hardest to drive headphones, and lastly it's a preamp for a home system. The Graham Slee Gram Amp II SE at around $400 is a KILLER phono stage for the money and likely has a cult following. It's been on the market for years, like the Decware Zen amps. Match this front end with any current Omega and you will have a system trouncing ones much more expensive.