When using the reply button at the bottom of topic, it's a reply to the opening post. When you use the reply button under a post, it's a reply to that post. This works well except for a reply to the last post.
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There is no visual indication if this was a reply to the last post or to the opening post. I know that it's a reply to the last post because it is marked like that in the notifications.
How does one differentiate as an other user?
Interesting question, I can agree it's a drawback. When you quote someone you can trace that post, but not with a plain reply.
@ledsyn You can, of course, always use @ to indicate that the reply is to a particular user
One could, but by simply referring to a user, will it show which post one is replying to?
I agree that it can cause ambiguities because the information about which post is being replied to is lost so the context is not always clear. Of course the author of the referenced post is notified but that is not generally visible.
I don't understand it myself, but it seems somewhat related to the issue that you cannot quote the last post completely without the system throwing away the text that you have just quoted, in a sort of post close editing operation. I suppose the principle is that a thread progresses linearly and there is only one "active" discussion point of focus at any one time. However, this is not necessarily true here where different groups of participants are discussing different aspects of the issue in parallel.
I never said that it did and I am sure that you know that.
If I want to indicate that I am replying to the last post in a topic then I try to make it clear by putting my reply in context
Or quote.
You see, you do know how to do it 
The context could, of course, include a quote. This is particularly the case when answering one of several questions
