We do not provide support for customer wired scenarios because this often leads to damaged actuators. Instead, we offer a plug-n-play solution that cannot be miswired. Again, the Japanese actuators are wired differently than those sold in the rest of the world.
Yes, the software does indeed talk to the USB interface. In the case of the SX-3000/Comander 3, it is an optimized USB driver from SimXperience rather than a generic driver. Had we allowed the Commander 3 to talk to the generic drivers, they would simply fail or be unreliable.
The advantage of us specifying both hardware and software allows ismuch better performance, reliability and far easier configuration. Notice, that here, you don't see 50 pages of forum threads about how to get an actuator communicating :)