Exactly. Basically replies are “kind 1” events, which are supported by the most popular clients like #Damus, #Amethyst and #Snort. So users of such clients see your reply as a new note. This is something that I believe should and probably will be addressed in the future.

At the same time Amethyst, unlike the rest of “general purpose” clients supports long-form posts - kind 30023 events - which allows its users to see the original posts. Hence, this makes your reply look like a reply.