Source control is fine in NoFlo's JSON graph format or DSL.
Which is fine, that is what I'd expect. It's how I'd implement it. But isn't that a huge clue about the fundamental weakness of graphical representation - as soon as you try to do anything nontrivial it's back to text. And back to text for a very good reason, not because the right git plugin hasn't been written yet.
One simple hack is to take each version, set transparency to 50%, and then overlay them.