First, I have to respectfully disagree that it is a misdeal when two or more boxed cards are found at any point during a hand is the standard rule. Although there has been some discussion as to whether or not the rule should be changed, I think the rules are actually clear that the two or more boxed cards must be found during the initial distribution of cards, and before substantial action pre-flop has taken place. In my opinion, the overriding general principle is absolutely clear: once action begins, a misdeal cannot be called (the exception being if the deck is 'fouled').
Since no action has yet to take place, it is easier at that point in time to "restart" the hand when two boxed cards are found or similarly, two cards are exposed by dealer error, during the initial distribution. At this point, no one is reasonably certain how many opponents there will be in the hand, what the betting will be like, whether they are favored to win, and so on. So this is a fine compromise rather than trying to force the deal continue.
Second, once the deal is started, any further boxed cards are treated as a scrap of paper. Even if there are 2, 4, 6 or 8 boxed cards found, the rule can be applied uniformly, and no subjective assessment is required. A misdeal, in my opinion, should not be called. One might say "well the player would have hit a flush, or would have hit trips", etc., but it was just as likely that a card that would not have helped might appear boxed, so I do not find that argument persuasive. My biggest concern is that if there is an automatic rule that says that there will be a misdeal upon finding a second boxed card in the middle of a hand, then it would be too easy for a rogue dealer to manipulate the deck to kill the hand. I would have the same concerns if there was a rule that a second card exposed anytime during a hand would result in a misdeal. Once there has been action, the hand is much more defined: we have limited the number of opponents, and there will be one player typically that is favored to win... sometimes they may even have the other player drawing dead. The hand should be permitted to proceed to completion. Calling a misdeal at this point can be highly prejudicial to the player most favored to win at that point. This is much different than discovering the boxed cards during the initial deal.
In summary, I would respectfully disagree with calling a misdeal in the situations that you describe. However, what I would support, is that if a boxed card is found at any point in the hand, that the floor should be permitted to ask the dealer to spread the deck to check for a second (or more) boxed cards. Since it is highly likely that a second boxed card will follow a first, and one player might be an advantage because it was his hand in a previous deal and only he knows the second card, then looking to see if there are other boxed cards before continuing would not advantage any particular player. But then, I would still insist that the hand proceed to completion after the check is done.