Logistically it wouldn't be a problem since, as you say, the Amiga motherboard has an ordinary ATX form factor and would be right at home in a PC shop. The problem would be finding shops that would want to bother with such an offbeat product and then making sure the shop staff understood what an AmigaOne is. This is where I think there'd be trouble getting shops to cooperate. The public is essentially ignorant about Amigas and most shops probably don't think it's worth their time to try to educate the masses. Added to the problem is the fact that there may not be much promotional support from Eyetech or whoever the distributor is in your region. All those big Intel stickers cost money, as do the brochures, in-store displays, staff training and so on. Small manufacturers would have trouble matching that level of support.
Maybe it'd be better to find local shops that already specialize in niche products. For example, near my office here in Tokyo is the outfit that Be, Inc. worked with to push BeOS in Japan.
Plat'Home carries Linux and BSD products, hardware, etc., so it was an easy thing to take on BeOS as well. I can imagine AmigaOnes (and Pegasos, too) being right at home there. The shop customers are people who are more sophisticated users than most, probably have already educated themselves about the products, etc.
When (or if) Amiga and Pegasos are more widely known then maybe more mainstream shops will see the potential for sales and will be more willing to carry the products.
BTW, for comparison purposes, Genesi is thinking more along the lines of viral grassroots sales with enthusiast users/developers setting up localized web sites to act as resellers and offer support, etc. Presumeably these local enthusiast resellers would have some boards and boxes on hand to let people play with, but I don't know how that's supposed to work for sure.
-- gary_c