Ahh yes, this is an interesting debate. I thought about both options and decided to go with the current system as it gives you more control. It should be easy enough to switch back and forth between the two, but my suggestions is to use “All Stories” for feeds and “Unread only” for folders. That way you can drill into feeds to get to stories you missed, but you can ignore read stories when reading by river.
Or just do what I do and have everything set to All Stories, since most of the time only unreads will be visible.
Neither of these options uses the intelligence control (what I call that all/unread/focus segmented control at the bottom of the feed list on both web and mobile). I think it’s too confusing to have what looks like a feed list control also affect the story list. So I split them up, which gives you more control.