Or lacking that, what does vagrant do so much better than the base tools on their own that you would never want to do without it?
As far as I can see you can do all that vagrant does with vboxmanage, vboxheadless and cloning. I generally ssh into my virtualboxes already.
You could even make an argument against vagrant - if you want to maintain the same deployment tools for vboxes and production boxes, so that you can rehearse/test initial deployment, deployment and recovery on a vbox configured as much as possible as a production box.
I'm more than open to correction or persuasion ...