In order to do signal processing like directing the bass to the sub or creating 5.1 from analog stereo, receivers convert to digital. Since the Anthem is primarily a video processor, it uses the sample rate that is most comment in video, namely 48 Khz. If it were a primarily audio device, then it might use 96 Khz or 192 KHz, but as a video device it uses 48 Khz.
Most people who are listening to high res music prefer to not have the analog converted to digital. That does mean that you only get output from 2 speakers, assuming it is a stereo signal. You need full range speakers for that. If you need to use a sub, then the stereo signal needs to be converted to digital.
So, to listen to pure 96 Khz, you need to do it in two channel mode with no processing. If you need the sub, then the analog signal needs to be converted to digital.