Yup. Straight to the bottom of the page. Did you know, they're pushing it into schools? Every time a student asks a question, all other students lose track of which pieces of work they've still got left to do.
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.
The intended Teams place for these things to be is either Assignments or the "_Content Library" section of a Class Notebook. Both of them are harder for teachers to use than a channel called "homework" (or just the main channel; creating a channel is hard, too).
I think this is actually a useful design feature - if the thread didn’t move and it was up in the message chain and I wasn’t tagged in a message then I would miss it, but as I want to still read everything in the channel, the fact it comes to the bottom of the channel means I see it.
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.
Wait, what? Do threads move when they get replies or something?