Hello Steven,
The boxed card can become a bit more complex in a stud type game, as opposed to a flop game. Imagine dealing the river card, in stud, and dealing past the boxed card...a misdeal would not be an option.
A boxed card during the initial deal of a flop game would be handled exactly the way Robert's Rules describes it...that is; it would be replaced by the card directly beneath it. If, however, the dealer deals beyond the boxed card and the next card is dealt the next (incorrect) player...I would consider a misdeal if substantial action has not occurred.
Keep in mind, the incidence of a boxed card is (or should be) a very, very, rare occurrence.
To answer your question more specifically, I guess it would depend on the type of game being played, and when the boxed card appears.
Good question.