When you shuffle the rest, the only place you can shuffle them into is into deck, because it just says "shuffle the rest," and not "shuffle the rest then put them on the bottom of your library." As such when you are shuffling the cards into the deck, that will shuffle your entire deck making the question moot.
The act of shuffling the cards requires them to be non-revealed, so once you start the shuffle, they have to be not revealed.
