Used to be, the factories went AMA Superbike racing by signing up an American go-fast shop and sending them the good stuff. It was a good way for the factories to get back into racing after they had pulled out in the 1980s.
Then racing went "in-house".
Honda absorbed the Commonwealth team. Yamaha split with Vance and Hines and moved their race shop to the company grounds at Cypress, California back in '97. Kawasaki and Rob Muzzy went their separate ways, too, after the 2000 season.
The lone factory team holdout to the old way in the US is Suzuki. They are contracted to Yoshimura R&D, just like they have been for decades, since Pops Yoshimura impressed the factory boys with his legendary tuning ability.
Suzuki has never fielded an in-house rae team in the US.
In-house teams allow the factories to control access to the super-secret technology. It also provides for cost control.
However, it's not lost on observers that Yoshimura Suzuki and Erion Honda (a factory supported team) lead all four AMA championships at the moment.
"In-house" factory teams win World Championship races every weekend and it's an effective way of running a competent squad. But there's more than one way to skin a cat or win a championship -- at least in the US where outsourcing is far from dead.