I am describing what I see on Element X on iOS today. If someone replies to threads, it is not hidden and navigable on this client. Even after switching the labs feature on, the app was showing the thread interspersed with the rest of the conversation.

Uninstalling the app, reinstalling, and making sure the labs option is turned on before navigating to a room with threads, is behaving how I expect.

So maybe, its a bug that the room does not re-render after toggling that setting.