It's worth mentioning that the three main on-line retailers of higher end recordings all have their own labels so in some cases they do manufacture, license, design artwork etc.
Acoustic Sounds=Analogue Productions & APO
Music Direct=Mobile Fidelity
Elusive Disc=Audio Wave
You are really comparing apples to oranges here - not that you are entirely wrong but the ecomomy of scale in this case works against the bigger company. Not that all are, but most SACD's retail at above $24.99 and in many cases $30 and above. Rhino's marketplace is traditional retail - where those pricepoints are certain death. Analogue can make 500 SACD's mark them up well over 100% and turn a profit. That business model does not exist even in the remotest sense at the major label level. Also it should be noted that all SACD is manufactured overseas where minimums are less and print is far less expensive than in US - even with exchange rates and freight factored in. Forget vinyl in the argument - even if it doubled or tripled it's current sales figures in the upcoming years it would still represent an insignifcant blip on the screen - profitable however for those that have a targeted consumer base - like the audiophile suppliers you mention.
Yes the major labels are inept and certainly should share significantly in the blame for the current state of affairs. This however has less to do with the mechanics of making and distributing records and more to do with the pressures of being owned by mulitnational corporations who care far less about art than commerce. Unfortunately, when you make crappy art commerce suffers. The real tragedy here is that the people who are passionate the most about the music at these companies are the ones who will be losing their gigs.