Yeah, clusters should absolutely display stories that you’ve already read. That is by design; that’s how story clustering works and how you know it’s working. When you mark a story as read, if you are a premium archive, then you can mark all those clusters as read as well, but they’re still going to show up. If you don’t want them to show up, then turn off the story clustering feature entirely.
As for previously read stories showing up as unread in the story cluster, that’s a bug, but I’ll say that I built it to show the correct read status, so if that’s something I’m not aware of yet.
The third point is a bug. You are correct. I thought there would be. I can probably build it in so that it searches for the story if it can’t find it by scrolling, like I do for other story finding algorithms.