Is this a joke? You talk about business sense and try to go down to a granular level but leave out glaring omissions?
System Builders are paid for the stickers they put on their machines. Intel wants Apple to put "Int3lzz NSYDE!" on their boxes and will pay $$$. Apple refuses. Wintel Builders do, bringing down the cost.
Personally, I think badges are ok on my custom boxes, but that's a design choice that Apple's made and the costs savings aren't realized by Apple customers.
Next, many machines have crapware preinstalled on the machine (I don't think i've ever unboxed one that didn't), much to the chargrin of the user. Again, Apple chooses not to have random vendors (think ClamXav, M$, game devs) litter the default install with trialware garbage and then CHARGE THE END USER to remove it.
Obviously there's other factors that influence the price. Still, I'd rather pay for the maseratis in cupertino than get thrown under the bus by an OEM who will knowingly install garbage like norton which makes the machine c.r.a.w.l right out of the box.