While I really like the Chat Replies, I think that I agree with the comments in https://twitch.uservoice.com/forums/310201-chat-messaging/suggestions/41117761-ability-to-turn-off-chat-reply-threads-feature saying that it can become really confusing and hard to moderate.

I think that in addition to that feature, there should be another option to limit Chat Replies to only the streamer / moderators as this would be extremely valuable in cases where there are Q&A sessions or where streamers want their moderation team to collate responses and maintain context of the response.

Thanks again, Twitch Team!