It was the same way with commenting in VaultWiki 3, in that you had to visit the wiki page to view them; however, you could find new wiki comments in the New Posts function, and it was only possible to have a single discussion going per wiki page. In the back-end, forum threads were used for the whole thing (page + discussion being a single thread), but it was presented the same way it is today; the wiki areas were the forums the threads were in, so it would not have been an improvement on your current predicament (existing forums with related threads).
When VaultWiki 4 was designed, vBulletin 4 was already being demoed with a unified activity stream, so the loss of the New Posts integration was deemed acceptable. The areas were moved away from the forums because as stated before, vBulletin made it a nightmare to do that way, and users had found it confusing to do it that way. However, a year later, XenForo came out and it had no unified activity, although it was easier to use forums/threads.