comment-reply.js always focuses on comment textarea

This is just good user experience (UX): When someone clicks on Comment or Answer, they have started writing their comment already in their mind. Don’t break that flow with secondary fields. This the reason why you should move the textarea to the top.

To change that, you could listen to document changes, check the comment fields to see if they exist, are empty and required, and if the commenter hasn’t started typing already. Then move the cursor. I strongly recommend not to do that.