Okay, this wasn't quite as terrible as I had assumed. There was an issue where the message area was not always HTML encoded, and that has been corrected.
The HTML block issue I was referring to was actually not a bug in vBulletin or VaultWiki at all, but another conflict with CES Parser Permissions, where it checks for banned HTML tags before the parser even has a chance to HTML the tags. Tags not in the banned tag list function properly. All this requires is an update to CES Parser Permissions.