I updated last night.
Multichannel playback for files copied back to the card works! Rebuilding a take for a fileset is super quick. One quirk, which is inconsequential as far as I can tell: If the file set contains the extra stereo file (say dig-in, or a live mix from the other channels), after a rebuild that file remains separate from the multichannel set. The machine will playback the files included in the multichannel take simultaneously, and once the end of the multichannel file is reached, the stereo file will play after it, sequentially, from the 1/2 RCA outputs and digital out.
This behavior is different than playing back files without (removing and) rebuilding the take. In that case the stereo file will not play sequentially after the multichannel files, but is accessed via the stereo/multi button on top of the machine. Switch back and forth between the multichannel set and the stereo file by pressing that button. Behaving like two parallel playlists rather than one playing the files in series.
In either case, the stereo file cannot be played simultaneously with the multichannel files, so this doesn't really matter. However once should be able to rename the stereo file 'st12, st34, or st56' to take the place of a stereo pair from the multichannel take, allowing it to be played back simultaneously with the others that way.