If you use the green Reply button associated within a post, then you are responding to that specific post.
If you scroll to the top (or bottom) of a thread and use the Reply All button, it doesn't associate your response to a specific post, it is just a general comment/response to the thread.
By the way, there are green triangles over on the right hand scroll bar that are shortcuts to quickly take you to the bottom or top of a page, much like holding down the control key and pressing either the Home or End key on your keyboard. It makes moving around the lengthy pages less of a chore.
The email notice function is not functioning at the moment. It got broken by the movers when we moved to this format version of the website. You've seen those videos of the FedEx driver tossing the box over the fence to deliver it? I think that's what the movers did with the email notice function.
Edit to respond to your edit: Yes, it adds the @poster to your reply so readers can click on it to see what you were responding to if it isn't in chronological order. The Reply All button does not add the @poster to your response.
You can also use the Quote Button to cite all or parts of the text in a post you are responding to.