The biggest problem with DVD-Audio is the copy protection associated with the format. Digital output is prohibited unless you use IEEE-1394 (FireWire), HDMI v1.1+, or a couple of manufacturer-specific proprietary connections (Denon Link being one example). As a result, you can't output a DVD-A bitstream over USB.

Also, the 990's USB input will work with PCM stereo but not with Dolby Digital or DTS bitstreams. When building your HTPC, you'll want to find a sound card with a digital output and driver support for digital bypass.