Google has changed how new app permissions are applied when updating Google Play apps. Previously, automatically updated apps displayed explicit details and required user confirmation when a new version gained additional privileges. Google Play no longer displays the addition of new privileges if a user has previously accepted any other permission in the same category as the new permission. This makes it possible for an app to sneak in permission changes without the user realising making the Android platform less secure.
It's also possible to restore most devices so that it is difficult or impossible to tell that they have been rooted. I think the only reason they tell you it voids the warranty is to scare you off.