I think the difference between our opinions is that you think it's acceptable to have metadata in files exposed to the user, and I think it's not, and indeed we'll have to agree to disagree on this one 
Or simpler, git has moved file detection and it isn't slow at all.
That's the heuristics I mentioned earlier and it's neither simple nor perfectly accurate. Git doesn't always detect that a file has been moved. And, for our purpose, if it's not 100% accurate we need to have an ID in the note file itself.