I can speak to this as I've been using Parinfer on existing code for the last week or so.
There can potentially be a "big diff" when you run Paren Mode on a file for the first time, but that's typically a one-time event. The beauty of Parinfer is that most Lisp code already uses these conventions.
Once you start using Parinfer's Indent Mode regularly it feels crazy to write or edit lisp without it.
One of my plans for atom-parinfer[0] is to have a comment flag in a file that will automatically signal "use Parinfer on this file". Similar to JSHint inline configurations [1].