You go to a lot of effort in that first part only to ultimately agree with me in your final sentence.
Aftermarket versions of the ZX6R fairing that are produced in much smaller numbers (and therefore have a higher per-unit manufacturing cost in addition to the costs of having to reverse engineer the factory mounting system) run
nearly $800. That's listed as no more than half the cost of factory parts, which means that you're looking at $1,600 for factory parts at the very least.
Given that the aftermarket companies can sell their versions for a profit at $800,
this suggests that Kawasaki is charging based on what the market will bear rather than simply costs plus a basic profit.
If a small aftermarket company with much higher per-unit production costs can sell painted and finished fairing kits for $800 and still make a profit, there's really no legitimate reason why Kawasaki couldn't sell OE fairings, painted and finished, for the same price and make more profit than the aftermarket company. No matter how much overheard Kawasaki has (and, since the majority of the overhear for Kawasaki is sunk cost because it's required for their other operations the actual cost that can be assigned to warehousing fairings is, in actuality, incredibly small), they still have superior efficiency to a small aftermarket supplier.
ZV