Apparently, the timecode modification is applied to the actual file, not just the file's representation on FCP (ie. not like a Subclip). Modifying the timecode manually could mean that you can't recapture, media manage etc. (which isn't really an issue if, say, you captured the original footage without a batchlist, using Capture Now, or used a non-controllable-timecode device), and that your clip timecode would have a discrepancy with what's on the tape.
How about this instead: Sync the two clips, then copy each clip separately into its own sequence. This means you'll have two sequences in perfect sync. Now cut them into a third sequence as nested clips and turn Timecode Overlays on. This should allow you to implement a "control" timecode (ie. the timecodes on the two sequences/nested clips, which are easily adjustable via sequence settings) to the two clips without changing the timecode on the clips themselves.
You could also apply a Timecode Generator to the synced clips, which gives you an actual onscreen readout of where you are on the timecode. Just make sure the Generator filters on the clips have identical numbers.
When I edit synced footage, I usually just lay one piece from each camera angle in sync, and then drag, drag, drag, razor.