It isn't so much as a reply on a re-tweet, if you comment or "reply" to any tweet then the layout is the same as any other social media site and nests it under the post. Whereas for re-tweeting it is more like sharing something, like a link or an article, and your desired message into a post, just like here in lemmy your title or message is at the top and your content is under it. In this context the tweet is your content.

I hope that made sense