I don’t think putting all the work for students to do is seen as the use case for teams channels - it’s for chat and discussion.

If you are trying to get students to do work, maybe use something like planner, sharepoint or any of the other myriad of tools actually designed for collaborative working rather than chat.

Apps like Slack solve this by having a dedicated “Threads” channel where you can see new messages in threads you’ve participated in. There’s also the concept of an “Activity” view where you can see recent activity in a channel, if I recall correctly. There’s no need to re-arrange message order or rewrite history to draw attention to new messages. Worst case, just insert a message visible only to you with a link to the thread when updates occur.