I think that is intended. The issue is the wording used by Flarum, they don't differentiate between a reply and a normal comment response. That extension looks like it requires a Reply to the original post itself, mentioning the author (on traditional forums this was what quoting was used for). The large Reply button and the box at the bottom simply add a comment response without mentioning anyone or anything.
The extensions looks like it requires a reply to the original post only, so the reply button on the post is the only option.
