The RF used on ANY universal remote -- such as the URC-9800 -- is NOT for control of RF devices. It is for RF control of IR-based devices, from the remote to the basestation to your devices. The reason that no remote controls can operate RF devices is because there is no standard -- everyone does their own thing.

So what it boils down to is that it'll be impossible for you to integrate control of your Bose system and the rest of your equipment into a single remote control, at least not until Bose comes out with a solution (which they don't seem keen on doing).