I start using the overlays for links, and experienced a few limitations around keyboarding while you're in an overlay:

• presentation navigation controls continue to work, but happy invisibly in the background; a couple of these controls are useful to have in overlay mode (e.g. space or arrow down in an iframe), hence, I'd say we should block those events while we're in an overlay.
• pausing the presentation still works in an overlay, but it is not visible since the overlay (z-index: 1000) sits on top of the pause (z-index: 100); either the feature should not work, or it should cover the overlay imo.