Make replies an extra tab
If you want to make it easier for users to follow a conversation (which is a good idea, even if this implementation seems messy), let their @ mentions be a separate tab that they can click into and see, rather than cluttering the main chat experience.
composeralex shared this idea
This could be a pop-up that appears when clicking a message in chat.
This would make it easier to have & read conversations in chat, while not having to introduce a new way to response to chat messages (people are already using @'s).