My concern with overlay scrollbars is that they don't seem to offer a clear affordance until the user has already taken steps to interact with them. The nub that fades in has the same feel to it as those flash websites that require you to mouse over all the graphics, just to see which ones will perform an action.

Existing scrollbars look like something in a track that you can move back and forth. Overlay scrollbars, particularly in iOS, aren't used to interact with the content. You move the content itself, the scrollbars are just indicators showing your position. They shouldn't look 'grab-able', because you never grab one.

The implementation shown in this post is grab-able, but doesn't look to be. I think that's a mistake.

(I should note, iOS is the only place I have experience with overlay scrollbars. I'm not qualified to discuss how they're used elsewhere. If other systems use them differently, please chime in.)