For what it’s worth, I like it as-is.
That way no matter how far down I am in the post, I can still reply to the original topic, or engage with any of the replies previously – and it’s my choice.
From my understanding, generic replies (sans-link) are either be replying to the post immediately above, OR to the original topic. Maybe I just want to reply/respond to the main topic (even after reading only 30/100 comments), and the reply button in the gutter is a good way of doing that. I think it’s fine to reply in general even if the user hasn’t read all the way to the bottom. It should perhaps be encouraged by the community, but not mandatory by the software.