To clarify, when you are listed as the 3rd or emergency QB(as AJ usually is if Koy is holding), you are not technically activated for the game. So if a situation arises and the 3rd QB needs to come in the game before the 4th quarter, neither the backup or starting QB can re-enter the game.
The Eagles situation is that since Koy must be on the active roster to be the holder, AJ Feeley has be technically deactivated. Therefore if Garcia were to be injured for a series or even two, Andy Reid would be forced to put Koy Detmer in the game to prevent the situation where Garcia could not return. Obviously this is not an ideal situation. By activating both Koy and AJ, either can come into the game at any time.
If the Eagles did not do this and Garcia were hurt for any length of time... Reid would have to decide whether to ride it out with Koy Detmer, or bring in AJ and prevent both Garcia and Detmer from returning... Again, not a good situation.
The drawback would be that one defensive back, lineman, linebacker, running back ect that the Eagles normally carry would have to be deactivated. That spot would probably come at the expense of a guy like Torrance Daniels or some other special teamer.
All in all, I can't disagree with Andy if he does this. There's no room for error now and it can't hurt to be prepared for the worst. You can win a playoff game with Koy Detmer and you don't want to change holders in the middle of a game.