We'll call my current vBulletin install account in WHM vbulletin, making the directory /home/vbulletin/public_html/.
If I were to create a XenForo user, that directory would be /home/xenforo/public_html and it would be completely clean.
Before the actual migration I could install XenForo and get it setup the way we need it, do the DB migration, then I could just point my domain to that new directory.
In my head this makes sense, any reason it doesn't? Is there a better way to do it, considering I want a 'clean install'?