I have thought a bit about this, but I tend to disagree because a) there’s no transparency about having used reply on a post vs. reply on a thread, and b) the behaviour is inconsistent between single and multiple replies. Also, as mentioned above, I also feel the behaviour is surprising, which is IMO not a good thing in terms of UX.
So I would argue that the default setting should be reversed and the reply indication should be shown also for single replies, with the option to turn this off if desired.
But I do appreciate you linking the Quick Quote theme component. My main concern there is that I consider it an advantage that Discourse discourages full quotes and encourages replies (with selective quotes as needed), because this keeps avoids (visual) duplication of existing content.