There's no clear right and wrong in issues like this but a few facts: nearly no high-end lines have margin of 50%. some cables, maybe. (Transparent springs to mind). Most gear is around 40%, maybe 45% if you pay the invoice in 7 days, etc. Video gear is even less, try like 30% or so. (TV's, etc.).
Ultimately if the retailers don't survive (somehow), the manufacturers don't survive = kiss goodbye the idea of high end in general. (taken to logical conclusion). Where do you think used/demo gear comes from?
"So, buying new at full MSRP also meant getting inferior performance for the necessary burn times." This is BS IMNSHO. burn in as a concept is overrated.
"However, 50% markups on items that they don't keep in stock and have to special order, seems out of line to me. " So tell us about your business. Do people know your margins? Do they beat you up on price about them? Is it justified in their eyes?
" Unfettered by the product lines you have to sell, you provide a far more level playing field of unbiased opinion." not really. There's plenty of dealers here masquerading as consumers, and pimping their stuff. Likewise, plenty of insecure buyers that like to reaffirm their purchase choices by talking them up. (and trash talking stuff they don't like.). Read between the lines and you will see this fairly often here, FWIW.
RE: whole-home system installation: It's a service like anything else, and there is a cost. Design may be free (or at least subsidised) but parts and labor never are. Skilled designers/installers don't come cheap and of course their labor is marked up by the store. Some stores stay afloat on their custom install departments... its' where the money is right now (along with Home Theater). 2-channel market is very slumped as far as retail goes.
Yes, I buy on Audiogon too, but I patronize my local dealers when I can and when it makes sense. No, I don't pay retail (who does?) but they make enough to keep in business and I enjoy having and advocate should the need arise (e.g. warranty issue, free loaner gear, in-home trial, etc.). The stores I go to have 7-day money back, 30-day exchange, and liberal (free) in-home trial of demo gear. IMHO, that's worth what margin they get on the stuff.
Just a little devil's advocation here.
-Ed