Yes, it covers the 'set', not individual cards. Mostly because you wouldn't selll the cards individually to people. As for the upgrade to a full deck, I think you have to contact the representative at the site to ask about that because you're substantially changing the amount of cards in the deck. I think it MIGHT be covered because the deck would still have the same name or title it would be sold under, but check to be sure. You can actually call a copyright lawyer to ask that, for free, and get an answer but I'd contact the copyright office first since they're far more familiar with how things work in regards to the VA form.
The $30 for example would cover an art portfolio if it was meant to be sold with all the pictures as a set, would cover a sculpture/artistic creation of Noah's Ark with all the pieces because it's considered a complete set, would cover a selection of songs in a music book because all the songs are bound together as a set in the book, etc.