Don't worry about the 3rd QB. Teams can keep a 3rd QB and he is protected but does not count against the 53 man roster. Only deal is that if the 3rd one is called up then the number 1 can not play that game.
I don't think it works that way. You're getting two rules mixed up. All active players count against the 53 man roster. During a game, if the third QB comes into the game (aka the emergency QB) the starting QB is no longer eligibile to re-enter the game.