I see the posts with all comments as replies, but it does take some navigation to see everything, like a twitter conversation. It's less intuitive than the nested comment layout but the content seems to be there.

What I'm really impressed by is being able to follow Lemmy communities from within Mastodon... e.g. by searching @technology@beehaw.org I can see threads and posts without leaving my Mastodon app of choice (Tusky). It's amazing how it just works.