Sorry if this suggestion has been made before, but can't vBulletin simply consider website.com and
www.website.com the same domain?
No other web software I've ever used has come across this problem. It seems like it's how vBulletin chooses its implementation. I'm sure there are reasons for it, but surely there is a better way to handle this, somehow, than requiring a .htaccess rewrite rule to be manually added to the website.