Hello:
That’s quite possible - looking at the file diffs and running a test just now, it looks like Logic is creating a graphic overview for the WAV file, then writing this to the end of original file, leaving the rest of it unchanged (save for a couple of bytes near the beginning). In doing so, it appears to be not updating the Modified Time of the file.
Sounds like my best bet is to back off the Fs Watcher Delay to give chance for the file to be completely written before it gets hashed - but it brings up an interesting question: what happens in Syncthing when an application updates a file without updating its Modified Time?