I tend to skim a bunch of articles, and make a mental note of the position of interesting ones to go back to later, but when I scroll up, everything is in a different location, breaking the mental map that I had built.
Other than that, I think it is a great alternative. Good work.
This type of feature is sometimes implemented as a huge green banner stickied to the bottom of the view but that I find that too obtrusive and stress inducing - I end up clicking on them to get them out of the way even when I don't want to see the new stories so it actually makes the experience worse. I prefer a more subtle indicator in the top-right similar to how notifications appear in some apps but it shouldn't feel like an error/warning or something that requires immediate attention.
The auto-refresh was making me crazy as well - even a big 'Auto-Refresh: ON' toggle by the menu would be enough.
I'm not a fan of settings in general but it does appear you're getting two distinct groups of users.
Then give the option to hide it, after you've made your selection. :)
Do not automatically change content that requires people to read