Actually, I think it depends. For example, if you make changes to a Contact Form that is on the home page, perhaps inserted by a short-code, WP Super Cache would have no idea that this form changed (since the content on the home page hasn’t actually changed — because the short code didn’t change). Also, if the Theme you are using stores changes as database entries in some random table, vs making an actual change to what’s listed in the Post, it may not cause a page flush. That said, if you have the “extra home page checks” checkbox checked (if you are running in “Advanced” mode) I believe it will eventually stop caching and check both the cached and uncached pages to see if they still match. The plugin authors certainly know more than I do, so I will let them further comment on this. But I think it’s a bit misleading to say “yes it should’ — yes, most of the time it should, but sometimes (depending on your Theme, or what was actually changed) it might not.
– Scott