It would be awesome if it didn’t mark posts as unread until you partially scrolled through them (like Google Reader).
Sometimes you click on one feed, get distracted, come back, and switch to another. In that case, I’d prefer to have the first post in the first feed still in an unread state.
Have you tried the new preference “Mark as read after X seconds”? That may be closer to what you’re looking for.
It’s close, but still feels a little awkward.
Another way to think about this would be to place the dorito slightly above the top of the feed pane. I don’t know how hard this would be to implement though.
This other thing I’ve noticed is that if you’re in the ‘show unread only’ mode, it’s sometimes impossible to scroll down to the last unread item(s) in a feed, so you have to mark them as read by clicking on them in the Story Titles pane. It would be nice if you could scroll all items passed the dorito, just revealing whitespace if there’s nothing else unread in the feed.
Yeah, I’ve noticed that as well. The way I get around it is to just hit the ‘down’ key to manually mark those stories as read. But adding some padding, the exact distance of the indicator to the bottom of the screen might do the trick. I’ll play with that.
OK, deployed. Let me know if that works better. 
It looks like the padding might be the distance from the indicator to the top of the pane (instead of the bottom). Chrome 21.0.1180.57 on OS X.