1) Nothing. It only effects certain zone assignments (not 100% sure on which ones). After selecting over the top or underneath, you can physically see what zone assignments have changed but (sometimes none, sometimes a couple - depending on the play). For example, I know if someone has that purple zone about 10 yards deep towards the sideline and you select underneath, you'll see that assignment change to light blue and covering the flat. That's one I know for sure.
2) Not that I've seen. I've seen my CB's physically change their positioning to shade inside/outside, but haven't noticed a change with my safeties.