There is a reply link on every node which you can use if you want to reply to a specific node, otherwise the comment-on link to reply to the original post.

This is mostly true. Replies hidden beyond the viewer's chosen depth don't have the reply link. Once the viewer clicks on a specific node to expand that part of the tree the selected node has a "Comment on" link rather than a "reply" link. It's possible this is a source of confusion for someone new to the interface, especially if English is not among their strongest skills.