Even if you can't read the values with JavaScript, you can submit the form with JavaScript.
So then you'd need to prompt the users to confirm that they want to auto fill, not just notify that auto fill happened. Otherwise it may already be too late.
Even if you couldn't read any hidden value with JS and had no way of telling if they changed (didn't try it myself) you could submit the form every 5-10 seconds or so in the background and reject it server side if a hidden field is missing.
