It's an odd rule, but I think people are thinking about it backwards.
NFL teams are allowed a 45 man active roster. Only players on the active roster are allowed to play in the game. The only exception to this is the 3rd quarterback. He does not count against the 45 man limit, but if you use him, you are not allowed to bring either of the two guys in front of him back into the game. An exception allows the guy to come in during the 4th quarter without restriction, ostensibly to get mop-up duty in blowouts, although that isn't clearly defined.
NFL rosters allow enough guys for 2 deep at every position, and they have added an emergency spot at QB in the rare case that the first two go down. It is the highest profile and arguably most important spot on the field, and it isn't really possible to cover with a guy from another spot.