Quite possibly, but having worked in the supply chain for the automotive industry, there are some parts where logistics and inventory management and such are really not set up to deliver a single unit to an end user. You cannot just walk down the the factory floor, grab a part off the conveyor, slap it in a FedEx box, and charge BOM cost plus shipping (unless you hate your own inventory people).
There's almost definitely some room for improvement, but given that the motherboard assembly is one of the most expensive parts of the console and you're adding irregular, small quantity shipments to a parts center not on the usual delivery route, the overhead of storage and repacking from bulk containers into individual boxes and operating the parts center, some margin to absorb the risk you get stuck with parts no one orders... full motherboard replacements are always gonna be questionable value.