So, looking into this, campaign files in the builder are really simple. They are basically save files that contain a list of official WotC game elements that are allowed in this campaign. You can filter the list by book (Martial Power, Dragon Magazine, etc) and then add or remove elements one by one from that book.
The idea is that a DM can choose to forbid certain game elements from play, or only allow stuff from the three core books or something. He could then create a custom campaign save using the builder, which his players would load. Then the characters created using that campaign save would only be able to take allowed rules elements.
For WotBS, this doesn't work because EnWorld doesn't specify what WotC stuff to use or not to use, the DM would still make that call. Adding the stuff in the Player's Guide is impossible because there's no way to tell the Builder what those elements actually do, what the requirements are, and so on. You can define them as house rules (click the little "H" icon on the top right when picking feats or whatever) but house rules in the builder are very basic and have no mechanical presence. They're basically just notes on your character sheet.
