I believe it has to do with the way the system checks the disc for verification key. With the hastily rewrite for the XB1 OS to no longer need the online check, they check to see if the disc for a game is in the system, and then launch the installed game. The disc functions as nothing more after the install other than to allow the system to launch. If the game had 2 discs, each one would be able to activate the game.

While it is reasonable to assume they will fix this in the future, it probably isn't worth the last minute effort right now so close to launch to do so. Then you also have to factor in people who don't have a connected console who would have to update their dash OS etc... I believe MCC will be reissued in the future with 2 discs, it's better for MS in the long term once they can make the necessary changes to the system OS.