Looks like they'll be doing some version of supporting bitstream over the hdmi or spdif interfaces while providing stereo pcm over analog at the same time.
http://jira.boxee.tv/browse/BOXEE-7337

But Eli's comment "Only work for Dolby Digital" is not great. I assume it means only Dolby Digital audio will be handled and all other audio will still not be

Given the abundance of non-Dolby Digital this seems ver incomplete even though Eli marked the issue Resolved