I just discovered this after shooting a documentary using a Zoom H4N. I think Time-of-day timecode is an excellent feature! (Although it would be nice of Zoom to document it!) It helps a lot with rough syncing. If you don’t like it, it’s easy to do a batch transcode in any software ignoring timecode, and it will make all the resulting files start at 00:00:00.
For my workflow, I transcoded all the original WAVs to MP3 to send to a translator/transcriber. These MP3s all started with zeroed timecode. So to match the transcriptions to the original audio, I added an Aux TC track to each audio file, making each one start at zero.
As Jeremy said earlier, to view this Aux timecode, you need to open each clip in the viewer, right-click the current timecode box, and select Aux TC. Surprisingly, this will affect the timecode overlays in the canvas. This is because the timecode track selection affects the master clip, therefore it affects all affiliate clips in any timeline.