When I was still working in the MC industry, I was seated with several Yamaha engineers at dinner when this very topic came up. Their reply was that rather than simply drain and replace the fork oil, which essentially left 90% of the dirt and grit in the fork tube to be re-distributed by the fresh oil, leaving the drain bolt out forced the mechanic to strip the fork, clean and inspect everything and then refill it. It's sound reasoning, but presumes that the majority of owners would have the job done properly by a qualified dealership. Emphasis on qualified.
They also had the attitude that as delivered the fork oil level and viscosity was perfect, and that the average owner wasn't qualified to make any changes. Anyone that's followed GP racing know how intractable some of those guys could be. Even Kenny Roberts had to fight with them to make suspension changes.
Once the big four got away with it, I think other manufactures adopted the practice because it probably saves two or three bucks a bike, which multiplied over a thousands of bikes production run saves real money.
As a side comment I have a shop owner friend that served a formal 4 year apprenticeship in Germany to become a licensed motorcycle mechanic. Over there when they changed the fork oil they inspected and cleaned everything the way the Yamaha engineers had envisioned. When he came to the US he was appalled at how lax the standards were in most dealerships, and at how many corners were cut by owners and mechanics alike.