KYB is nothing special either (I'm not a fan of their car shocks either, over damped and harsh). Some of the 39 mm forks Harley used came from KYB early on. They build what the manufacturer specifies and is willing to pay for. If the manufacturer wants to pay for premium quality components, KYB, Showa or anyone else can build it. If the OEM only wants low quality components then that is what they get. If the OEM doesn't have a budget for engineering and testing, then the resulting suspension settings, damping and spring rates, may be poorly chosen. Also keep in mind that bikes are set up for a notional "median" rider. If you weight more or less than this notional character, carry a passenger all the time or routinely carry a lot of cargo in saddlebags and/or a tank bag, then the stock suspension probably won't work well for you even with the most expensive and exotic suspension components.
Keep in mind the OEM works with the suspension supplier to get the spring and damping rates they want for their motorcycle, or car. It isn't a case of Harley going to Endurance, or Showa or KYB and saying I need forks or shocks for this or that bike. Harley or BMW or whomever spends time with the suspension supplier testing different suspension settings to get the components to perform to the bike manufacturers requirements. Now, how much money the manufacturer is willing to spend on testing and how much they are willing to spend on hardware qualtiy determines how well the production machine performs. I would be wary of a blanket assumption that just because Harley is using Endurance the suspension is necessarily bad. Maybe not. It depends on how much time and money Harley invested on engineering and testing and what quality materials Harley was willing to pay for.