Are you talking about the sidebar here, or hiding in the main outline view as well? I agree the sidebar needs work and I commented some here. But in the main view I think you can just collapse the Archive so you will see it, but not what it contains?
It is possible to write a script to archive to a separate file. I know there have been scripts for TaskPaper 2 and maybe FoldingText that do this, not sure if one exists yet for TaskPaper 3. See if any of my ideas in the other thread seem like they would work. Otherwise I can help you get a script together that archives to a separate document.