You can probably account for that by applying a more specific class just for this situation and applying it after the code that implements auto-saving.

Except you can use feature detection rather than waiting for the all the JS to finish. Something like:

const { classList } = document.documentElement;

if ('fetch' in window) {
  classList.add('fetch-available');
} else {
  classList.add('js');
}

Granted, this won’t help if, say, fetch is available but the network is down; but then again, you loaded the page in the first place, so you’re most of the way there.